Differentiation of pluripotent stem cells

ABSTRACT

The present invention is directed to methods to differentiate pluripotent stem cells. In particular, the present invention is directed to methods and compositions to differentiate pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage comprising culturing the pluripotent stem cells in medium comprising a sufficient amount of GDF-8 to cause the differentiation of the pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage.

This application is a continuation application of U.S. patent application Ser. No. 13/434,409, filed on Mar. 29, 2012 (now U.S. Pat. No. 9,593,306, issued Mar. 14, 2017), which is a continuation application of U.S. patent application Ser. No. 12/494,789, filed Jun. 30, 2009 (now abandoned), which claims priority to U.S. Provisional Application No. 61/076,900, filed Jun. 30, 2008, U.S. Provisional Application No. 61/076,908, filed Jun. 30, 2008, and U.S. Provisional Application No. 61/076,915, filed Jun. 30, 2008, all of which are herein incorporated by reference in their entirety.

FIELD OF THE INVENTION

The present invention is directed to methods to differentiate pluripotent stem cells. In particular, the present invention is directed to methods and compositions to differentiate pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage comprising culturing the pluripotent stem cells in medium comprising a sufficient amount of GDF-8 to cause the differentiation of the pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage.

BACKGROUND

Advances in cell-replacement therapy for Type I diabetes mellitus and a shortage of transplantable islets of Langerhans have focused interest on developing sources of insulin-producing cells, or β cells, appropriate for engraftment. One approach is the generation of functional β cells from pluripotent stem cells, such as, for example, embryonic stem cells.

In vertebrate embryonic development, a pluripotent cell gives rise to a group of cells comprising three germ layers (ectoderm, mesoderm, and endoderm) in a process known as gastrulation. Tissues such as, for example, thyroid, thymus, pancreas, gut, and liver, will develop from the endoderm, via an intermediate stage. The intermediate stage in this process is the formation of definitive endoderm. Definitive endoderm cells express a number of markers, such as, for example, HNF-3beta, GATA4, MIXL1, CXCR4 and SOX17.

Formation of the pancreas arises from the differentiation of definitive endoderm into pancreatic endoderm. Cells of the pancreatic endoderm express the pancreatic-duodenal homeobox gene, PDX1. In the absence of PDX1, the pancreas fails to develop beyond the formation of ventral and dorsal buds. Thus, PDX1 expression marks a critical step in pancreatic organogenesis. The mature pancreas contains, among other cell types, exocrine tissue and endocrine tissue. Exocrine and endocrine tissues arise from the differentiation of pancreatic endoderm.

Cells bearing the features of islet cells have reportedly been derived from embryonic cells of the mouse. For example, Lumelsky et al. (Science 292:1389, 2001) report differentiation of mouse embryonic stem cells to insulin-secreting structures similar to pancreatic islets. Soria et al. (Diabetes 49:157, 2000) report that insulin-secreting cells derived from mouse embryonic stem cells normalize glycemia in streptozotocin-induced diabetic mice.

In one example, Hori et al. (PNAS 99: 16105, 2002) discloses that treatment of mouse embryonic stem cells with inhibitors of phosphoinositide 3-kinase (LY294002) produced cells that resembled β cells.

In another example, Blyszczuk et al. (PNAS 100:998, 2003) reports the generation of insulin-producing cells from mouse embryonic stem cells constitutively expressing Pax4.

Micallef et al. reports that retinoic acid can regulate the commitment of embryonic stem cells to form Pdx1 positive pancreatic endoderm. Retinoic acid is most effective at inducing Pdx1 expression when added to cultures at day 4 of embryonic stem cell differentiation during a period corresponding to the end of gastrulation in the embryo (Diabetes 54:301, 2005).

Miyazaki et al. reports a mouse embryonic stem cell line over-expressing Pdx1. Their results show that exogenous Pdx1 expression clearly enhanced the expression of insulin, somatostatin, glucokinase, neurogenin3, p48, Pax6, and HNF6 genes in the resulting differentiated cells (Diabetes 53: 1030, 2004).

Skoudy et al. reports that activin A (a member of the TGF-β superfamily) up-regulates the expression of exocrine pancreatic genes (p48 and amylase) and endocrine genes (Pdx1, insulin, and glucagon) in mouse embryonic stem cells.

The maximal effect was observed using 1 nM activin A. They also observed that the expression level of insulin and Pdx1 mRNA was not affected by retinoic acid; however, 3 nM FGF7 treatment resulted in an increased level of the transcript for Pdx1 (Biochem. J. 379: 749, 2004).

Shiraki et al. studied the effects of growth factors that specifically enhance differentiation of embryonic stem cells into Pdx1 positive cells. They observed that TGFβ2 reproducibly yielded a higher proportion of Pdx1 positive cells (Genes Cells. 2005 June; 10(6): 503-16).

Gordon et al. demonstrated the induction of brachyury [positive]/HNF-3beta [positive] endoderm cells from mouse embryonic stem cells in the absence of serum and in the presence of activin along with an inhibitor of Wnt signaling (US 2006/0003446A 1).

Gordon et al. (PNAS, Vol 103, page 16806, 2006) states: “Wnt and TGF-beta/nodal/activin signaling simultaneously were required for the generation of the anterior primitive streak.”

However, the mouse model of embryonic stem cell development may not exactly mimic the developmental program in higher mammals, such as, for example, humans.

Thomson et al. isolated embryonic stem cells from human blastocysts (Science 282:114, 1998). Concurrently, Gearhart and coworkers derived human embryonic germ (hEG) cell lines from fetal gonadal tissue (Shamblott et al., Proc. Natl. Acad. Sci. USA 95:13726, 1998). Unlike mouse embryonic stem cells, which can be prevented from differentiating simply by culturing with Leukemia Inhibitory Factor (LIF), human embryonic stem cells must be maintained under very special conditions (U.S. Pat. No. 6,200,806; WO 99/20741; WO 01/51616).

D'Amour et al. describes the production of enriched cultures of human embryonic stem cell-derived definitive endoderm in the presence of a high concentration of activin and low serum (D'Amour K A et al. 2005). Transplanting these cells under the kidney capsule of mice resulted in differentiation into more mature cells with characteristics of some endodermal organs. Human embryonic stem cell-derived definitive endoderm cells can be further differentiated into PDX1 positive cells after addition of FGF-10 (US 2005/0266554A1).

D'Amour et al. (Nature Biotechnology 24, 1392-1401 (2006)) states: “We have developed a differentiation process that converts human embryonic stem (hES) cells to endocrine cells capable of synthesizing the pancreatic hormones insulin, glucagon, somatostatin, pancreatic polypeptide and ghrelin. This process mimics in vivo pancreatic organogenesis by directing cells through stages resembling definitive endoderm, gut-tube endoderm, pancreatic endoderm and endocrine precursor en route to cells that express endocrine hormones.”

In another example, Fisk et al. reports a system for producing pancreatic islet cells from human embryonic stem cells (US2006/0040387A1). In this case, the differentiation pathway was divided into three stages. Human embryonic stem cells were first differentiated to endoderm using a combination of n-butyrate and activin A. The cells were then cultured with TGF-β antagonists such as Noggin in combination with EGF or betacellulin to generate PDX1 positive cells. The terminal differentiation was induced by nicotinamide.

In one example, Benvenistry et al. states: “We conclude that over-expression of PDX1 enhanced expression of pancreatic enriched genes, induction of insulin expression may require additional signals that are only present in vivo” (Benvenistry et al., Stem Cells 2006; 24:1923-1930).

Activin A is a TGF-beta family member that exhibits a wide range of biological activities including regulation of cellular proliferation and differentiation, and promotion of neuronal survival. Isolation and purification of activin A is often complex and can often result in poor yields. For example, Pangas, S. A. and Woodruff, T. K states: “Inhibin and activin are protein hormones with diverse physiological roles including the regulation of pituitary FSH secretion. Like other members of the transforming growth factor-β gene family, they undergo processing from larger precursor molecules as well as assembly into functional dimers. Isolation of inhibin and activin from natural sources can only produce limited quantities of bioactive protein.” (J. Endocrinol. 172 (2002) 199-210).

In another example, Arai, K. Y. et al. states: “Activins are multifunctional growth factors belonging to the transforming growth factor-β superfamily. Isolation of activins from natural sources requires many steps and only produces limited quantities. Even though recombinant preparations have been used in recent studies, purification of recombinant activins still requires multiple steps.” (Protein Expression and Purification 49 (2006) 78-82).

Therefore, there still remains a significant need for alternatives for activin A to facilitate the differentiation of pluripotent stem cells.

SUMMARY

In one embodiment, the present invention provides a method to differentiate pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage, comprising culturing the pluripotent stem cells in medium comprising a sufficient amount of GDF-8 to cause the differentiation of the pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage.

In one embodiment, the medium comprising a sufficient amount of GDF-8 also contains at least one other compound. In one embodiment, the at least one other compound is an aniline-pyridinotriazine. In an alternate embodiment, the at least one other compound is a cyclic aniline-pyridinotriazine.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A and FIG. 1B shows the differentiation of H1 human embryonic stem cells into cells expressing markers characteristic of the definitive endoderm lineage. Differentiation was determined by measuring cell number (FIG. 1A) and SOX17 intensity (FIG. 1B) using an IN Cell Analyzer 1000 (GE Healthcare). Human embryonic stem cells were treated for a total of four days with medium containing 20 ng/ml Wnt3a plus activin A at the concentrations indicated (black bars) or medium lacking Wnt3a but with activin A at the concentrations indicated (white bars).

FIG. 2 shows the dose response relationship of activin A and GDF-8 used to differentiate cells of the human embryonic stem cell line H1 toward cells expressing markers characteristic of the definitive endoderm lineage. Cells were treated for a total of three days with activin A or GDF-8 at the concentrations shown in combination with 20 ng/ml Wnt3a on the first day of assay. Differentiation was determined by measuring SOX17 intensity using a fluorescent antibody probe and high content analysis on a GE Healthcare IN Cell Analyzer.

FIG. 3 shows the expression of CXCR4 in cells following the first step of differentiation, according to the methods described in Example 12. H1 cells were treated with 100 ng/ml activin A or 200 ng/ml GDF-8 for a total of three days in combination with 20 ng/ml Wnt3a for the first day or 2.5 μM Compound 34 or 2.5 μM Compound 56 for all three days. CXCR4 expression was measured using a fluorescent antibody probe and flow cytometry, yielding the percentages of positive cells shown.

FIG. 4 shows the expression of SOX17 in cells after three days differentiation to definitive endoderm according to the methods described in Example 12. H1 cells were treated for a total of three days with 100 ng/ml activin A or 200 ng/ml GDF-8 in combination with 20 ng/ml Wnt3a for the first day or 2.5 μM Compound 34 or 2.5 μM Compound 56 for all three days. Differentiation was determined by measuring SOX17 intensity (black bars) and resulting cell number (white bars) with fluorescent antibody probes and high content analysis on a GE Healthcare IN Cell Analyzer.

FIG. 5 shows the expression of PDX1 and CDX2 protein in cells following the third step of differentiation, according to the methods described in Example 12. H1 cells were treated for a total of three days with 100 ng/ml activin A or 200 ng/ml GDF-8 in combination with 20 ng/ml Wnt3a for the first day or 2.5 μM Compound 34 or 2.5 μM Compound 56 for all three days followed by subsequent differentiation through the second and third steps of differentiation. Protein expression and cell numbers, as determined with fluorescent antibody probes and high content analysis, are depicted for each treatment group. For comparative purposes, values are normalized relative to treatment with activin A/Wnt3a.

FIG. 6 shows the expression of PDX1 protein (white bars) and cell number (black bars) in cells following the fourth step of differentiation, according to the methods described in Example 12. H1 cells were treated for a total of three days with 100 ng/ml activin A or 200 ng/ml GDF-8 in combination with 20 ng/ml Wnt3a for the first day or 2.5 μM Compound 34 or 2.5 μM Compound 56 for all three days followed by subsequent differentiation through the second, third, and fourth steps of differentiation. Protein expression and cell numbers, as determined with fluorescent antibody probes and high content analysis, are depicted for each treatment group. For comparative purposes, values are normalized relative to treatment with activin A/Wnt3a.

FIG. 7 shows the protein expression for insulin and glucagon and cell number in cells differentiated according to the methods described in Example 12. H1 cells were treated for a total of three days with 100 ng/ml activin A or 200 ng/ml GDF-8 in combination with 20 ng/ml Wnt3a for the first day or 2.5 μM Compound 34 or 2.5 μM Compound 56 for all three days followed by subsequent differentiation through the second, third, fourth, and fifth steps of differentiation. Protein expression and cell numbers, as determined with fluorescent antibody probes and high content analysis, are depicted for each treatment group. For comparative purposes, values are normalized relative to treatment with activin A/Wnt3a.

FIG. 8A to FIG. 8G show SOX17 protein expression and cell number in human embryonic stem cells after differentiation to definitive endoderm, according to the methods described in Example 13. H1 cells were treated for a total of four days with 100 ng/ml of activin A or 100 ng/ml of a GDF-growth factor in combination with 20 ng/ml Wnt3a for the first day or 2.5 μM Compound 34 or 2.5 μM Compound 56 for the first two days of assay. SOX17 protein expression (black bars) and cell numbers (white bars), as determined with fluorescent antibody probes and high content analysis, are depicted for each treatment group. For comparative purposes, values are normalized relative to treatment with activin A/Wnt3a. FIG. 8A shows a series of control conditions for differentiation in the absence of any growth factors (NONE), or with activin A/Wnt3a treatment (AA/Wnt3a) or with individual reagents alone.

FIG. 8B shows differentiation with GDF-3, alone or in multiple combinations with Wnt3a, Compound 34, or Compound 56. FIG. 8C shows differentiation with GDF-5, alone or in multiple combinations with Wnt3a, Compound 34, or Compound 56. FIG. 8D shows differentiation with GDF-8, alone or in multiple combinations with Wnt3a, Compound 34, or Compound 56. FIG. 8E shows differentiation with GDF-10, alone or in multiple combinations with Wnt3a, Compound 34, or Compound 56. FIG. 8F shows differentiation with GDF-11, alone or in multiple combinations with Wnt3a, Compound 34, or Compound 56. FIG. 8G shows differentiation with GDF-15, alone or in multiple combinations with Wnt3a, Compound 34, or Compound 56.

FIG. 9A to 9G show SOX17 protein expression in human embryonic stem cells after differentiation to definitive endoderm, according to the methods described in Example 14. H1 cells were treated for a total of three days with 100 ng/ml of activin A or various growth factors at the concentrations shown in combination with 20 ng/ml Wnt3a or 2.5 μM Compound 34 for the first day of assay. SOX17 protein expression (black bars) and cell numbers (white bars), as determined with fluorescent antibody probes and high content analysis, are depicted for each treatment group. For comparative purposes, values are normalized relative to treatment with activin A/Wnt3a. FIG. 9A shows a series of control conditions for differentiation with Wnt3a alone or in the absence of any growth factors (None) or with activin A/Wnt3a treatment (AA/Wnt3a). FIG. 9B shows differentiation with GDF-8 (Vendor PeproTech), at the concentrations shown, in combination with 20 ng/ml Wnt3a. FIG. 9C shows differentiation with GDF-8 (Vendor Shenendoah), at the concentrations shown, in combination with 20 ng/ml Wnt3a. FIG. 9D shows differentiation with TGFβ1, at the concentrations shown, in multiple combinations with Wnt3a or Compound 34. FIG. 9E shows differentiation with BMP2, at the concentrations shown, in multiple combinations with Wnt3a or Compound 34. FIG. 9F shows differentiation with BMP3, at the concentrations shown, in multiple combinations with Wnt3a or Compound 34. FIG. 9G shows differentiation with BMP4, at the concentrations shown, in multiple combinations with Wnt3a or Compound 34.

FIG. 10 shows SOX17 protein expression in human embryonic stem cells after differentiation to definitive endoderm, according to the methods described in Example 15. H1 cells were treated for a total of three days in various timed exposures with 100 ng/ml of activin A or 100 ng/ml GDF-8 in combination with 20 ng/ml Wnt3a. SOX17 protein expression, as determined with fluorescent antibody probes and high content analysis, is shown as total intensity values for each treatment group, testing control conditions for differentiation with no growth factors added (no treatment), with Wnt3a alone, with activin A or GDF-8 alone, or with activin A/Wnt3a treatment or GDF-8/Wnt3a treatment, where Wnt3a was added only for the first day of assay or for all three days of assay as shown.

FIG. 11A to FIG. 11G show SOX17 protein expression in human embryonic stem cells after differentiation to definitive endoderm, according to the methods described in Example 15. H1 cells were treated for a total of three days in various timed exposures with 100 ng/ml of activin A in combination with test compound (Compound 181 (FIG. 11A), Compound 180 (FIG. 11B), Compound 19 (FIG. 11C), Compound 202 (FIG. 11D), Compound 40 (FIG. 11E), Compound 34 (FIG. 11F), or GSK3 inhibitor BIO (FIG. 11G)) at the concentrations shown, where test compound was added only on the first day of assay. Protein expression for SOX17, as determined with fluorescent antibody probes and high content analysis, is depicted by total intensity values.

FIG. 12A to FIG. 12G show SOX17 protein expression in human embryonic stem cells after differentiation to definitive endoderm, according to the methods described in Example 15. H1 cells were treated for a total of three days in various timed exposures with 100 ng/ml of activin A in combination with test compound (Compound 181 (FIG. 12A), Compound 180 (FIG. 12B), Compound 19 (FIG. 12C), Compound 202 (FIG. 12D), Compound 40 (FIG. 12E), Compound 34 (FIG. 12F), or GSK3 inhibitor BIO (FIG. 12G)) at the concentrations shown, where test compound was added for all three days of assay. Protein expression for SOX17, as determined with fluorescent antibody probes and high content analysis, is depicted by total intensity values.

FIG. 13A to FIG. 13G show SOX17 protein expression in human embryonic stem cells after differentiation to definitive endoderm, according to the methods described in Example 15. H1 cells were treated for a total of three days in various timed exposures with 100 ng/ml of GDF-8 in combination with test compound (Compound 181 (FIG. 13A), Compound 180 (FIG. 13B), Compound 19 (FIG. 13C), Compound 202 (FIG. 13D), Compound 40 (FIG. 13E), Compound 34 (FIG. 13F), or GSK3 inhibitor BIO (FIG. 13G)) at the concentrations shown, where test compound was added only on the first day of assay. Protein expression for SOX17, as determined with fluorescent antibody probes and high content analysis, is depicted by total intensity values.

FIG. 14A to FIG. 14G show SOX17 protein expression in human embryonic stem cells after differentiation to definitive endoderm, according to the methods described in Example 15. H1 cells were treated for a total of three days in various timed exposures with 100 ng/ml of GDF-8 in combination with test compound (Compound 181 (FIG. 14A), Compound 180 (FIG. 14B), Compound 19 (FIG. 14C), Compound 202 (FIG. 14D), Compound 40 (FIG. 14E), Compound 34 (FIG. 14F), or GSK3 inhibitor BIO (FIG. 14G)) at the concentrations shown, where test compound was added for all three days of assay. Protein expression for SOX17, as determined with fluorescent antibody probes and high content analysis, is depicted by total intensity values.

FIG. 15 shows cell number yields after differentiation of human embryonic stem cells to definitive endoderm, according to the methods described in Example 15. H1 cells were treated for a total of three days in various timed exposures with 100 ng/ml of activin A or 100 ng/ml GDF-8 in combination with 20 ng/ml Wnt3a. Cell numbers, as determined with a fluorescent nuclear probe and high content analysis, are shown for each treatment group, testing control conditions for differentiation with no growth factors added (no treatment), with Wnt3a alone, with activin A or GDF-8 alone, or with activin A/Wnt3a treatment or GDF-8/Wnt3a treatment, where Wnt3a was added only for the first day of assay or for all three days of assay as shown.

FIG. 16A to FIG. 16G show cell number yields after differentiation of human embryonic stem cells to definitive endoderm, according to the methods described in Example 15. H1 cells were treated for a total of three days in various timed exposures with 100 ng/ml of activin A in combination with test compound (Compound 181 (FIG. 16A), Compound 180 (FIG. 16B), Compound 19 (FIG. 16C), Compound 202 (FIG. 16D), Compound 40 (FIG. 16E), Compound 34 (FIG. 16F), or GSK3 inhibitor BIO (FIG. 16G)) at the concentrations shown, where test compound was added only on the first day of assay. Cell number yields, as determined with a fluorescent nuclear probe and high content analysis, are shown.

FIG. 17A to FIG. 17G show cell number yields after differentiation of human embryonic stem cells to definitive endoderm, according to the methods described in Example 15. H1 cells were treated for a total of three days in various timed exposures with 100 ng/ml of activin A in combination with test compound (Compound 181 (FIG. 17A), Compound 180 (FIG. 17B), Compound 19 (FIG. 17C), Compound 202 (FIG. 17D), Compound 40 (FIG. 17E), Compound 34 (FIG. 17F), or GSK3 inhibitor BIO (FIG. 17G)) at the concentrations shown, where test compound was added for all three days of assay. Cell number yields, as determined with a fluorescent nuclear probe and high content analysis, are shown.

FIG. 18A to FIG. 18G show cell number yields after differentiation of human embryonic stem cells to definitive endoderm, according to the methods described in Example 15. H1 cells were treated for a total of three days in various timed exposures with 100 ng/ml of GDF-8 in combination with test compound (Compound 181 (FIG. 18A), Compound 180 (FIG. 18B), Compound 19 (FIG. 18C), Compound 202 (FIG. 18D), Compound 40 (FIG. 18E), Compound 34 (FIG. 18F), or GSK3 inhibitor BIO (FIG. 18G)) at the concentrations shown, where test compound was added only on the first day of assay. Cell number yields, as determined with a fluorescent nuclear probe and high content analysis, are shown.

FIG. 19A to FIG. 19C show cell number yields after differentiation of human embryonic stem cells to definitive endoderm, according to the methods described in Example 15. H1 cells were treated for a total of three days in various timed exposures with 100 ng/ml of GDF-8 in combination with test compound (Compound 181 (FIG. 19A), Compound 180 (FIG. 19B), Compound 19 (FIG. 19C), Compound 202 (FIG. 19D), Compound 40 (FIG. 19E), Compound 34 (FIG. 19F), or GSK3 inhibitor BIO (FIG. 19G)) at the concentrations shown, where test compound was added for all three days of assay. Cell number yields, as determined with a fluorescent nuclear probe and high content analysis, are shown.

FIG. 20A to FIG. 20F show the expression of various protein markers in cells throughout multiple steps of differentiation according to the methods described in Example 16. H1 cells were treated with 100 ng/ml activin A or 100 ng/ml GDF-8 for a total of three days in combination with 20 ng/ml Wnt3a for the first day or 2.5 μM various compounds (Compound 19, Compound 202, Compound 40, or GSK3 inhibitor BIO) added only on the first day. FIG. 20A shows FACS analysis for the definitive endoderm marker, CXCR4, in cells after the first step of differentiation. CXCR4 expression was measured using a fluorescent antibody probe and flow cytometry, yielding the percentages of positive cells as shown. FIG. 20B shows high content image analysis for normalized SOX17 protein expression (black bars) and recovered cell numbers (white bars) resulting from the first step of differentiation, testing the corresponding treatments shown. FIG. 20C shows high content image analysis for relative cell numbers recovered from cultures treated through differentiation step 5. FIG. 20D shows high content image analysis for glucagon protein expression from cultures treated through differentiation step 5. FIG. 20E shows high content image analysis for insulin protein expression from cultures treated through differentiation step 5. FIG. 20F shows the ratio of glucagon to insulin expression in cells from cultures treated through differentiation step 5. For comparison purposes, expression values in panels B, C, D, E, and F are normalized to the control treatment with activin A and Wnt3a during step 1.

FIG. 21A to FIG. 21N show the expression of various protein and RT-PCR markers in cells throughout multiple steps of differentiation according to the methods described in Example 17. H1 cells were treated with 100 ng/ml activin A or 100 ng/ml GDF-8 for a total of three days in combination with 20 ng/ml Wnt3a for the first day or various compounds at the following concentrations (Compound 181, Compound 180, Compound 19, Compound 202, Compound 40, Compound 56, or GSK3 inhibitor BIO) added only on the first day. FACS analysis for the definitive endoderm marker, CXCR4, is shown in cells after the first step of differentiation where treatment combined activin A (FIG. 21A) or GDF-8 (FIG. 21B) with Wnt3a or various compounds. CXCR4 expression was measured using a fluorescent antibody probe and flow cytometry, yielding the percentages of positive cells as shown. In subsequent panels of FIG. 21, normalized RT-PCR values for various differentiation markers are shown with respective treatments using activin A or GDF-8 during the first step of differentiation as follows: markers at the end of step one of differentiation for treatments combining activin A (FIG. 21C) or GDF-8 (FIG. 21D); markers at the end of step three of differentiation for treatments combining activin A (FIG. 21E) or GDF-8 (FIG. 21F); markers at the end of step four of differentiation for treatments combining activin A (FIG. 21G) or GDF-8 (FIG. 21H); markers at the end of step five of differentiation for treatments combining activin A (FIG. 21I) or GDF-8 (FIG. 21J). At the conclusion of step five of differentiation, high content analysis was performed to measure recovered cell numbers for corresponding treatments during the first step of differentiation using activin A (FIG. 21K) or GDF-8 (FIG. 21M). High content analysis was also used to measure glucagon and insulin intensity in recovered cell populations at the end of step five of differentiation, corresponding to treatment with activin A (FIG. 21L) or GDF-8 (FIG. 21N) during the first step of differentiation.

FIG. 22A and FIG. 22B show the expression of various protein and RT-PCR markers in cells treated according to the methods described in Example 18. H1 cells were treated with 100 ng/ml activin A or 100 ng/ml GDF-8 for a total of three days in combination with 20 ng/ml Wnt3a for the first day or 2.5 μM Compound 40 or 2.5 μM Compound 202 only on the first day. FIG. 22A shows FACS analysis for the definitive endoderm marker, CXCR4, in cells after the first step of differentiation. CXCR4 expression was measured using a fluorescent antibody probe and flow cytometry, yielding the percentages of positive cells as shown. In FIG. 22B, normalized RT-PCR values for various differentiation markers in cells recovered after the fourth step of differentiation are shown corresponding to respective treatments using activin A/Wnt3a or GDF-8/Compound 40 or GDF-8/Compound 202 during the first step of differentiation.

FIG. 23A to FIG. 23C show the level of C-peptide detected in SCID-beige mice that received cells at the end of step four of the differentiation protocol as described in Example 18.

FIG. 24A shows the expression of CXCR4, as determined by FACS in cells at the end of step one of the differentiation protocol described in Example 19. FIG. 24B shows the expression of various genes, as determined by RT-PCR in cells at the end of step four of the differentiation protocol described in Example 19. Two different experimental replicates are shown (Rep-1 and Rep-2), each subjected to identical treatment protocols. FIG. 24C shows the level of C-peptide detected in SCID-beige mice that received cells at the end of step four of the differentiation protocol as treated with GDF-8 and Wnt3a during the first step of in vitro differentiation. FIG. 24D shows the level of C-peptide detected in SCID-beige mice that received cells at the end of step four of the differentiation protocol as treated with GDF-8 and Compound 28 during the first step of in vitro differentiation.

FIG. 25A and FIG. 25B show the cell number (FIG. 24A) and expression of CXCR4 (FIG. 24B) from cells grown on microcarrier beads, treated according to the methods of the present invention as described in Example 22. Cells were grown on Cytodex3 beads without treatment (undifferentiated) or with treatment combining 100 ng/ml activin A with 20 ng/ml Wnt3a (AA/Wnt3a) or with various treatments combining GDF-8 as shown: 50 ng/ml GDF-8 with 2.5 μM Compound 34 (Cmp 34+8); or 50 ng/ml GDF-8 with 2.5 μM Compound 34 and 50 ng/ml PDGF (Cmp 34+8+D); or 50 ng/ml GDF-8 with 2.5 μM Compound 34 and 50 ng/ml PDGF and 50 ng/ml VEGF (Cmp 34+8+D+V); or 50 ng/ml GDF-8 with 2.5 μM Compound 34 and 50 ng/ml PDGF and 50 ng/ml VEGF and 20 ng/ml muscimol (Cmp 34+8+D+V+M).

FIG. 26A to FIG. 26I show the proliferation of cells following treatment of the compounds of the present invention as described in Example 23. FIG. 26A shows OD490 reading for all control treatments over the three-day assay period. FIG. 26B through FIG. 26I show assay results for treatment using a compound in combination with GDF-8 and measuring MTS OD readings at 1 day, 2 days, and 3 days after initiating the differentiation assay.

FIG. 27A to FIG. 27F show the expression of various proteins and genes from cells grown on microcarrier beads, treated according to the methods of the present invention. FIG. 27A shows the percent positive expression of CXCR4, CD99, and CD9 as determined by FACS in cells at the end of step one of the differentiation protocol described in Example 24. FIG. 27B shows cells recovered from treatments as shown differentiated through step three of the differentiation protocol. FIG. 27C shows ddCT values for various gene markers expressed in cells treated as shown in step and differentiated through step three of the protocol. FIG. 27E and FIG. 27F show ddCT values for various gene markers expressed at Stage 4.

DETAILED DESCRIPTION

For clarity of disclosure, and not by way of limitation, the detailed description of the invention is divided into the following subsections that describe or illustrate certain features, embodiments, or applications of the present invention.

Definitions

Stem cells are undifferentiated cells defined by their ability at the single cell level to both self-renew and differentiate to produce progeny cells, including self-renewing progenitors, non-renewing progenitors, and terminally differentiated cells. Stem cells are also characterized by their ability to differentiate in vitro into functional cells of various cell lineages from multiple germ layers (endoderm, mesoderm and ectoderm), as well as to give rise to tissues of multiple germ layers following transplantation and to contribute substantially to most, if not all, tissues following injection into blastocysts.

Stem cells are classified by their developmental potential as: (1) totipotent, meaning able to give rise to all embryonic and extraembryonic cell types; (2) pluripotent, meaning able to give rise to all embryonic cell types; (3) multipotent, meaning able to give rise to a subset of cell lineages but all within a particular tissue, organ, or physiological system (for example, hematopoietic stem cells (HSC) can produce progeny that include HSC (self-renewal), blood cell restricted oligopotent progenitors, and all cell types and elements (e.g., platelets) that are normal components of the blood); (4) oligopotent, meaning able to give rise to a more restricted subset of cell lineages than multipotent stem cells; and (5) unipotent, meaning able to give rise to a single cell lineage (e.g., spermatogenic stem cells).

Differentiation is the process by which an unspecialized (“uncommitted”) or less specialized cell acquires the features of a specialized cell such as, for example, a nerve cell or a muscle cell. A differentiated or differentiation-induced cell is one that has taken on a more specialized (“committed”) position within the lineage of a cell. The term “committed”, when applied to the process of differentiation, refers to a cell that has proceeded in the differentiation pathway to a point where, under normal circumstances, it will continue to differentiate into a specific cell type or subset of cell types, and cannot, under normal circumstances, differentiate into a different cell type or revert to a less differentiated cell type. De-differentiation refers to the process by which a cell reverts to a less specialized (or committed) position within the lineage of a cell. As used herein, the lineage of a cell defines the heredity of the cell, i.e., which cells it came from and what cells it can give rise to. The lineage of a cell places the cell within a hereditary scheme of development and differentiation. A lineage-specific marker refers to a characteristic specifically associated with the phenotype of cells of a lineage of interest and can be used to assess the differentiation of an uncommitted cell to the lineage of interest.

“β-cell lineage” refers to cells with positive gene expression for the transcription factor PDX-1 and at least one of the following transcription factors: NGN3, NKX2.2, NKX6.1, NEUROD, ISL1, HNF-3 beta, MAFA, PAX4, or PAX6. Cells expressing markers characteristic of the β cell lineage include cells.

“Cells expressing markers characteristic of the definitive endoderm lineage”, or “Stage 1 cells”, or “Stage 1”, as used herein, refers to cells expressing at least one of the following markers: SOX17, GATA4, HNF-3 beta, GSC, CER1, Nodal, FGF8, Brachyury, Mix-like homeobox protein, FGF4 CD48, eomesodermin (EOMES), DKK4, FGF17, GATA6, CXCR4, C-Kit, CD99, or OTX2. Cells expressing markers characteristic of the definitive endoderm lineage include primitive streak precursor cells, primitive streak cells, mesendoderm cells and definitive endoderm cells.

“Cells expressing markers characteristic of the pancreatic endoderm lineage”, as used herein, refers to cells expressing at least one of the following markers: PDX1, HNF-1 beta, PTF1 alpha, HNF6, or HB9. Cells expressing markers characteristic of the pancreatic endoderm lineage include pancreatic endoderm cells, primitive gut tube cells, and posterior foregut cells.

“Cells expressing markers characteristic of the pancreatic endocrine lineage”, or “Stage 5 cells”, or “Stage 5”, as used herein, refers to cells expressing at least one of the following markers: NGN3, NEUROD, ISL1, PDX1, NKX6.1, PAX4, or PTF-1 alpha. Cells expressing markers characteristic of the pancreatic endocrine lineage include pancreatic endocrine cells, pancreatic hormone expressing cells, and pancreatic hormone secreting cells, and cells of the β-cell lineage.

“Definitive endoderm”, as used herein, refers to cells which bear the characteristics of cells arising from the epiblast during gastrulation and which form the gastrointestinal tract and its derivatives. Definitive endoderm cells express the following markers: HNF-3 beta, GATA4, SOX-17, Cerberus, OTX2, goosecoid, C-Kit, CD99, or MIXL1.

“Extraembryonic endoderm”, as used herein, refers to a population of cells expressing at least one of the following markers: SOX7, AFP, or SPARC.

“Markers”, as used herein, are nucleic acid or polypeptide molecules that are differentially expressed in a cell of interest. In this context, differential expression means an increased level for a positive marker and a decreased level for a negative marker. The detectable level of the marker nucleic acid or polypeptide is sufficiently higher or lower in the cells of interest compared to other cells, such that the cell of interest can be identified and distinguished from other cells using any of a variety of methods known in the art.

“Mesendoderm cell”, as used herein, refers to a cell expressing at least one of the following markers: CD48, eomesodermin (EOMES), SOX17, DKK4, HNF-3 beta, GSC, FGF17, or GATA-6.

“Pancreatic endocrine cell”, or “pancreatic hormone expressing cell”, as used herein, refers to a cell capable of expressing at least one of the following hormones: insulin, glucagon, somatostatin, and pancreatic polypeptide.

“Pancreatic endoderm cell”, or “Stage 4 cells”, or “Stage 4”, as used herein, refers to a cell capable of expressing at least one of the following markers: NGN3, NEUROD, ISL1, PDX1, PAX4, or NKX2.2.

“Pancreatic hormone producing cell”, as used herein, refers to a cell capable of producing at least one of the following hormones: insulin, glucagon, somatostatin, and pancreatic polypeptide.

“Pancreatic hormone secreting cell”, as used herein, refers to a cell capable of secreting at least one of the following hormones: insulin, glucagon, somatostatin, and pancreatic polypeptide.

“Posterior foregut cell” or “Stage 3 cells”, or “Stage 3”, as used herein, refers to a cell capable of secreting at least one of the following markers: PDX1, HNF1, PTF-1 alpha, HNF6, HB-9, or PROX-1.

“Pre-primitive streak cell”, as used herein, refers to a cell expressing at least one of the following markers: Nodal, or FGF8.

“Primitive gut tube cell” or “Stage 2 cells”, or “Stage2”, as used herein, refers to a cell capable of secreting at least one of the following markers: HNF1, HNF-4 alpha.

“Primitive streak cell”, as used herein, refers to a cell expressing at least one of the following markers: Brachyury, Mix-like homeobox protein, or FGF4.

Isolation, Expansion, and Culture of Pluripotent Stem Cells Characterization of Pluripotent Stem Cells

The pluripotency of pluripotent stem cells can be confirmed, for example, by injecting cells into severe combined immunodeficient (SCID) mice, fixing the teratomas that form using 4% paraformaldehyde, and then examining them histologically for evidence of cell types from the three germ layers. Alternatively, pluripotency may be determined by the creation of embryoid bodies and assessing the embryoid bodies for the presence of markers associated with the three germinal layers.

Propagated pluripotent stem cell lines may be karyotyped using a standard G-banding technique and compared to published karyotypes of the corresponding primate species. It is desirable to obtain cells that have a “normal karyotype,” which means that the cells are euploid, wherein all human chromosomes are present and not noticeably altered.

Sources of Pluripotent Stem Cells

The types of pluripotent stem cells that may be used include established lines of pluripotent cells derived from tissue formed after gestation, including pre-embryonic tissue (such as, for example, a blastocyst), embryonic tissue, or fetal tissue taken any time during gestation, typically but not necessarily before approximately 10 to 12 weeks gestation. Non-limiting examples are established lines of human embryonic stem cells or human embryonic germ cells, such as, for example, the human embryonic stem cell lines H1, H7, and H9 (WiCell). Also contemplated is use of the compositions of this disclosure during the initial establishment or stabilization of such cells, in which case the source cells would be primary pluripotent cells taken directly from the source tissues. Also suitable are cells taken from a pluripotent stem cell population already cultured in the absence of feeder cells. Also suitable are mutant human embryonic stem cell lines, such as, for example, BG01v (BresaGen, Athens, Ga.).

In one embodiment, human embryonic stem cells are prepared as described by Thomson et al. (U.S. Pat. No. 5,843,780; Science 282:1145, 1998; Curr. Top. Dev. Biol. 38:133 ff., 1998; Proc. Natl. Acad. Sci. U.S.A. 92:7844, 1995).

In one embodiment, pluripotent stem cells are prepared as described by Takahashi et al. (Cell 131: 1-12, 2007).

Culture of Pluripotent Stem Cells

In one embodiment, pluripotent stem cells are typically cultured on a layer of feeder cells that support the pluripotent stem cells in various ways. Alternatively, pluripotent stem cells are cultured in a culture system that is essentially free of feeder cells but nonetheless supports proliferation of pluripotent stem cells without undergoing substantial differentiation. The growth of pluripotent stem cells in feeder-free culture without differentiation is supported using a medium conditioned by culturing previously with another cell type. Alternatively, the growth of pluripotent stem cells in feeder-free culture without differentiation is supported using a chemically defined medium.

The pluripotent stem cells may be plated onto a suitable culture substrate. In one embodiment, the suitable culture substrate is an extracellular matrix component, such as, for example, those derived from basement membrane or that may form part of adhesion molecule receptor-ligand couplings. In one embodiment, the suitable culture substrate is MATRIGEL® (Becton Dickenson). MATRIGEL® is a soluble preparation from Engelbreth-Holm-Swarm tumor cells that gels at room temperature to form a reconstituted basement membrane.

Other extracellular matrix components and component mixtures are suitable as an alternative. Depending on the cell type being proliferated, this may include laminin, fibronectin, proteoglycan, entactin, heparan sulfate, and the like, alone or in various combinations.

The pluripotent stem cells may be plated onto the substrate in a suitable distribution and in the presence of a medium that promotes cell survival, propagation, and retention of the desirable characteristics. All these characteristics benefit from careful attention to the seeding distribution and can readily be determined by one of skill in the art.

Suitable culture media may be made from the following components, such as, for example, Dulbecco's modified Eagle's medium (DMEM), Gibco #11965-092; Knockout Dulbecco's modified Eagle's medium (KO DMEM), Gibco #10829-018; Ham's F12/50% DMEM basal medium; 200 mM L-glutamine, Gibco #15039-027; non-essential amino acid solution, Gibco 11140-050; β-mercaptoethanol, Sigma # M7522; human recombinant basic fibroblast growth factor (bFGF), Gibco #13256-029.

Formation of Pancreatic Hormone Producing Cells from Pluripotent Stem Cells

In one embodiment, the present invention provides a method for producing pancreatic hormone producing cells from pluripotent stem cells, comprising the steps of:

-   -   a. Culturing pluripotent stem cells,     -   b. Differentiating the pluripotent stem cells into cells         expressing markers characteristic of the definitive endoderm         lineage,     -   c. Differentiating the cells expressing markers characteristic         of the definitive endoderm lineage into cells expressing markers         characteristic of the pancreatic endoderm lineage, and     -   d. Differentiating the cells expressing markers characteristic         of the pancreatic endoderm lineage into cells expressing markers         characteristic of the pancreatic endocrine lineage.

In one aspect of the present invention, the pancreatic endocrine cell is a pancreatic hormone producing cell. In an alternate aspect, the pancreatic endocrine cell is a cell expressing markers characteristic of the β-cell lineage. A cell expressing markers characteristic of the β-cell lineage expresses PDX1 and at least one of the following transcription factors: NGN3, NKX2.2, NKX6.1, NEUROD, ISL1, HNF-3 beta, MAFA, PAX4, or Pax6. In one aspect of the present invention, a cell expressing markers characteristic of the β-cell lineage is a β-cell.

Pluripotent stem cells suitable for use in the present invention include, for example, the human embryonic stem cell line H9 (NIH code: WA09), the human embryonic stem cell line H1 (NIH code: WA01), the human embryonic stem cell line H7 (NIH code: WA07), and the human embryonic stem cell line SA002 (Cellartis, Sweden). Also suitable for use in the present invention are cells that express at least one of the following markers characteristic of pluripotent cells: ABCG2, cripto, CD9, FOXD3, Connexin43, Connexin45, OCT4, SOX2, Nanog, hTERT, UTF-1, ZFP42, SSEA-3, SSEA-4, Tra1-60, or Tra1-81.

The pluripotent stem cells may be cultured on a feeder cell layer. Alternatively, the pluripotent stem cells may be cultured on an extracellular matrix. The extracellular matrix may be a solubilized basement membrane preparation extracted from mouse sarcoma cells (as sold by BD Biosciences under the trade name MATRIGEL™). Alternatively, the extracellular matrix may be growth factor-reduced MATRIGEL™. Alternatively, the extracellular matrix may be fibronectin. In an alternate embodiment, the pluripotent stem cells are cultured and differentiated on tissue culture substrate coated with human serum.

The extracellular matrix may be diluted prior to coating the tissue culture substrate. Examples of suitable methods for diluting the extracellular matrix and for coating the tissue culture substrate may be found in Kleinman, H. K., et al., Biochemistry 25:312 (1986), and Hadley, M. A., et al., J. Cell. Biol. 101:1511 (1985).

In one embodiment, the extracellular matrix is MATRIGEL™. In one embodiment, the tissue culture substrate is coated with MATRIGEL™ at a 1:10 dilution. In an alternate embodiment, the tissue culture substrate is coated with MATRIGEL™ at a 1:15 dilution. In an alternate embodiment, the tissue culture substrate is coated with MATRIGEL™ at a 1:30 dilution. In an alternate embodiment, the tissue culture substrate is coated with MATRIGEL™ at a 1:60 dilution.

In one embodiment, the extracellular matrix is growth factor-reduced MATRIGEL™. In one embodiment, the tissue culture substrate is coated with growth factor-reduced MATRIGEL™ at a 1:10 dilution. In an alternate embodiment, the tissue culture substrate is coated with growth factor-reduced MATRIGEL™ at a 1:15 dilution. In an alternate embodiment, the tissue culture substrate is coated with growth factor-reduced MATRIGEL™ at a 1:30 dilution. In an alternate embodiment, the tissue culture substrate is coated with growth factor-reduced MATRIGEL™ at a 1:60 dilution.

Markers characteristic of the definitive endoderm lineage are selected from the group consisting of SOX17, GATA4, HNF-3 beta, GSC, CER1, Nodal, FGF8, Brachyury, Mix-like homeobox protein, FGF4 CD48, eomesodermin (EOMES), DKK4, FGF17, GATA6, CXCR4, C-Kit, CD99, and OTX2. Suitable for use in the present invention is a cell that expresses at least one of the markers characteristic of the definitive endoderm lineage. In one aspect of the present invention, a cell expressing markers characteristic of the definitive endoderm lineage is a primitive streak precursor cell. In an alternate aspect, a cell expressing markers characteristic of the definitive endoderm lineage is a mesendoderm cell. In an alternate aspect, a cell expressing markers characteristic of the definitive endoderm lineage is a definitive endoderm cell.

Markers characteristic of the pancreatic endoderm lineage are selected from the group consisting of PDX1, HNF-1 beta, PTF1 alpha, HNF6, HB9 and PROX1. Suitable for use in the present invention is a cell that expresses at least one of the markers characteristic of the pancreatic endoderm lineage. In one aspect of the present invention, a cell expressing markers characteristic of the pancreatic endoderm lineage is a pancreatic endoderm cell.

Markers characteristic of the pancreatic endocrine lineage are selected from the group consisting of NGN3, NEUROD, ISL1, PDX1, NKX6.1, PAX4, and PTF-1 alpha. In one embodiment, a pancreatic endocrine cell is capable of expressing at least one of the following hormones: insulin, glucagon, somatostatin, and pancreatic polypeptide. Suitable for use in the present invention is a cell that expresses at least one of the markers characteristic of the pancreatic endocrine lineage. In one aspect of the present invention, a cell expressing markers characteristic of the pancreatic endocrine lineage is a pancreatic endocrine cell. The pancreatic endocrine cell may be a pancreatic hormone expressing cell. Alternatively, the pancreatic endocrine cell may be a pancreatic hormone secreting cell.

Formation of Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage

In one aspect of the present invention, pluripotent stem cells may be differentiated into cells expressing markers characteristic of the definitive endoderm lineage by culturing the pluripotent stem cells in medium comprising a sufficient amount of GDF-8 to cause the differentiation of the pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage.

The pluripotent stem cells may be cultured in the medium containing a sufficient amount of GDF-8 for about one day to about seven days. Alternatively, the pluripotent stem cells may be cultured in the medium containing a sufficient amount of GDF-8 for about one day to about six days. Alternatively, the pluripotent stem cells may be cultured in the medium containing a sufficient amount of GDF-8 for about one day to about five days. Alternatively, the pluripotent stem cells may be cultured in the medium containing a sufficient amount of GDF-8 for about one day to about four days. Alternatively, the pluripotent stem cells may be cultured in the medium containing a sufficient amount of GDF-8 for about one day to about three days. Alternatively, the pluripotent stem cells may be cultured in the medium containing a sufficient amount of GDF-8 for about one day to about two days. Alternatively, the pluripotent stem cells may be cultured in the medium containing a sufficient amount of GDF-8 for about one day.

In one embodiment, the GDF-8 is used at a concentration from about 5 ng/ml to about 500 ng/ml. In an alternate embodiment, the GDF-8 is used at a concentration from about 5 ng/ml to about 50 ng/ml. In an alternate embodiment, the GDF-8 is used at a concentration from about 5 ng/ml to about 25 ng/ml. In an alternate embodiment, the GDF-8 is used at a concentration of about 25 ng/ml.

In one embodiment, the medium comprising a sufficient amount of GDF-8 also contains at least one other factor. In one embodiment, the at least one other factor is selected from the group consisting of: EGF, FGF4, PDGF-A, PDGF-B, PDGF-C, PDGF-D, VEGF, muscimol, PD98059, LY294002, U0124, U0126, and sodium butyrate.

In one embodiment, the EGF is used at a concentration from about 5 ng/ml to about 500 ng/ml. In an alternate embodiment, the EGF is used at a concentration from about 5 ng/ml to about 50 ng/ml. In an alternate embodiment, the EGF is used at a concentration of about 50 ng/ml.

In one embodiment, the FGF4 is used at a concentration from about 5 ng/ml to about 500 ng/ml. In an alternate embodiment, the FGF4 is used at a concentration from about 5 ng/ml to about 50 ng/ml. In an alternate embodiment, the FGF4 is used at a concentration of about 50 ng/ml.

In one embodiment, the PDGF-A is used at a concentration from about 5 ng/ml to about 500 ng/ml. In an alternate embodiment, the PDGF-A is used at a concentration from about 5 ng/ml to about 50 ng/ml. In an alternate embodiment, the PDGF-A is used at a concentration of about 50 ng/ml.

In one embodiment, the PDGF-B is used at a concentration from about 5 ng/ml to about 500 ng/ml. In an alternate embodiment, the PDGF-B is used at a concentration from about 5 ng/ml to about 50 ng/ml. In an alternate embodiment, the PDGF-B is used at a concentration of about 50 ng/ml.

In one embodiment, the PDGF-C is used at a concentration from about 5 ng/ml to about 500 ng/ml. In an alternate embodiment, the PDGF-C is used at a concentration from about 5 ng/ml to about 50 ng/ml. In an alternate embodiment, the PDGF-C is used at a concentration of about 50 ng/ml.

In one embodiment, the PDGF-D is used at a concentration from about 5 ng/ml to about 500 ng/ml. In an alternate embodiment, the PDGF-D is used at a concentration from about 5 ng/ml to about 50 ng/ml. In an alternate embodiment, the PDGF-D is used at a concentration of about 50 ng/ml.

In one embodiment, the VEGF is used at a concentration from about 5 ng/ml to about 500 ng/ml. In an alternate embodiment, the VEGF is used at a concentration from about 5 ng/ml to about 50 ng/ml. In an alternate embodiment, the VEGF is used at a concentration of about 50 ng/ml.

In one embodiment, the muscimol is used at a concentration from about 1 μM to about 200 μM. In an alternate embodiment, the muscimol is used at a concentration from about 1 μM to about 20 μM. In an alternate embodiment, the muscimol is used at a concentration of about 20 μM.

In one embodiment, the PD98059 is used at a concentration from about 0.1 μM to about 10 μM. In an alternate embodiment, the PD98059 is used at a concentration from about 0.1 μM to about 1 μM. In an alternate embodiment, the PD98059 is used at a concentration of about 1 μM.

In one embodiment, the LY294002 is used at a concentration from about 0.25 μM to about 25 μM. In an alternate embodiment, the LY294002 is used at a concentration from about 0.25 μM to about 2.5 μM. In an alternate embodiment, the LY294002 is used at a concentration of about 2.5 μM.

In one embodiment, the U0124 is used at a concentration from about 0.1 μM to about 10 μM. In an alternate embodiment, the U0124 is used at a concentration from about 0.1 μM to about 1 μM. In an alternate embodiment, the U0124 is used at a concentration of about 1 μM.

In one embodiment, the U0126 is used at a concentration from about 0.1 μM to about 10 μM. In an alternate embodiment, the U0126 is used at a concentration from about 0.1 μM to about 1 μM. In an alternate embodiment, the U0126 is used at a concentration of about 1 μM.

In one embodiment, the sodium butyrate is used at a concentration from about 0.05 μM to about 5 μM. In an alternate embodiment, the sodium butyrate is used at a concentration from about 0.05 μM to about 0.5 μM. In an alternate embodiment, the sodium butyrate is used at a concentration of about 0.5 μM.

In an alternate embodiment, the at least one other factor is selected from the group consisting of: an aniline-pyridinotriazine, a cyclic aniline-pyridinotriazine, N-{[1-(Phenylmethyl)azepan-4-yl]methyl}-2-pyridin-3-ylacetamide, 4-{[4-(4-{[2-(Pyridin-2-ylamino)ethyl]amino}-1,3,5-triazin-2-yl)pyridin-2-yl]oxy}butan-1-ol, 3-({3-[4-({2-[Methyl(pyridin-2-yl)amino]ethyl}amino)-1,3,5-triazin-2-yl]pyridin-2-yl}amino)propan-1-ol, N˜4˜-[2-(3-Fluorophenyl)ethyl]-N˜2˜-[3-(4-methylpiperazin-1-yl)propyl]pyrido[2,3-d]pyrimidine-2,4-diamine, 1-Methyl-N-[(4-pyridin-3-yl-2-{[3-(trifluoromethyl)phenyl]amino}-1,3-thiazol-5-yl)methyl]piperidine-4-carboxamide, 1,1-Dimethylethyl {2-[4-({5-[3-(3-hydroxypropyl)phenyl]-4H-1,2,4-triazol-3-yl}amino)phenyl]ethyl}carbamate, 1,1-Dimethylethyl {[3-({5-[5-(3-hydroxypropyl)-2-(methyloxy)phenyl]-1,3-oxazol-2-yl}amino)phenyl]methyl}carbamate, 1-({5-[6-({4-[(4-Methylpiperazin-1-yl)sulfonyl]phenyl}amino)pyrazin-2-yl]thiophen-2-yl}methyl)piperidin-4-ol, 1-({4-[6-({4-[(4-Methylpiperazin-1-yl)sulfonyl]phenyl}amino)pyrazin-2-yl]thiophen-2-yl}methyl)piperidine-4-carboxamide, and 2-{[4-(1-Methylethyl)phenyl]amino}-N-(2-thiophen-2-ylethyl)-7,8-dihydropyrido[4,3-d]pyrimidine-6(5H)-carboxamide.

The Compounds of the Present Invention

The present invention provides compounds that are capable of differentiating pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage.

In one embodiment, the compound that is capable of differentiating pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage is an aniline-pyridinotriazine of the Formula (1):

The N-oxide forms, the pharmaceutically acceptable addition salts and the stereochemically isomeric forms thereof, wherein:

m represents an integer from 1 to 4; n represents an integer from 1 to 4; Z represents N or C;

R¹ and R⁸ each independently represent hydrogen, Het¹⁴, cyano, halo, hydroxy, C₁₋₆alkoxy-, C₁₋₆alkyl-, mono- or di(C₁₋₄alkyl)amino-carbonyl-, mono- or di(C₁₋₄alkyl)amino-sulfonyl, C₁₋₆alkoxy-substituted with halo or R¹ represents C₁₋₆alkyl substituted with one or where possible two or more substituents selected from hydroxy or halo;

R² and R⁹ each independently represents hydrogen, C₁₋₄alkyl, C₂₋₄alkenyl, Het³, Het⁴-C₁₋₄alkylcarbonyl-, mono- or di(C₁₋₄alkyl)amino-C₁₋₄alkyl-carbonyl- or phenyl optionally substituted with one or where possible two or more substituents selected from hydrogen, hydroxy, amino or C₁₋₄alkyloxy-;

R³ and R⁷ each independently represent hydrogen, C₁₋₄alkyl, Het⁶, Het⁷-C₁₋₄alkyl-, C₂₋₄alkenylcarbonyl-optionally substituted with Het⁸-C₁₋₄alkylaminocarbonyl-, C₂₋₄alkenylsulfonyl-, C₁₋₄lkyloxyC₁₋₄alkyl- or phenyl optionally substituted with one or where possible two or more substituents selected from hydrogen, hydroxy, amino or C₁₋₄alkyloxy-;

R4, R5, R6 and R¹⁰ each independently represent hydrogen or C₁₋₄alkyl optionally substituted with hydroxy, Het⁹ or C₁₋₄alkyloxy;

Het¹ and Het² each independently represent a heterocycle selected from pyrrolidinyl, piperidinyl, piperazinyl, pyridinyl, pyrimidinyl, pyrazinyl, imidazolidinyl or pyrazolidinyl wherein said Het¹ and Het² are optionally substituted with amino, hydroxy, C₁₋₄alkyl, hydroxy-C₁₋₄alIcyl-, phenyl, phenyl-C₁₋₄alkyl-, C₁₋₄alkyl-oxy-C₁₋₄alkyl-mono- or di(C₁₋₄alkyl) amino- or amino-carbonyl-;

Het³ and Het⁶ each independently represent, heterocycle selected from pyrrolidinyl or piperidinyl wherein said Het³ and Het⁶ are optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-;

Het⁴, Het⁷ and Het⁹ each independently represent a heterocycle selected from morpholinyl, pyrrolidinyl, piperazinyl or piperidinyl wherein said Het⁴, Het⁷ and Het⁹ are optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-;

Het⁵ represents a heterocycle selected from morpholinyl, pyrrolidinyl, piperazinyl or pipendinyl wherein said Het⁵ is optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-;

Het¹⁰, Het¹¹ and Het¹³ each independently represent a heterocycle selected from pyrrolidinyl, piperidinyl, piperazinyl, pyridinyl, pyrimidinyl, pyrazinyl, imidazolidinyl or pyrazolidinyl wherein said Het¹⁰, Het¹¹ and Het¹³ are optionally substituted with amino, hydroxy, C₁₋₄alkyl, hydroxy-C₁₋₄alkyl-, phenyl, phenyl-C₁₋₄alkyl-, C₁₋₄alkyl-oxy-C₁₋₄alkyl-, amino-carbonyl- or mono- or di(C₁₋₄alkyl)amino-;

Het¹² represents a heterocycle selected from pyrrolidinyl, piperidinyl, piperazinyl, pyridinyl, pyrimidinyl, pyrazinyl, imidazolidinyl or pyrazolidinyl wherein said Het¹² is optionally substituted with amino, hydroxy, C₁₋₄alkyl, hydroxy-C₁₋₄alkyl-, phenyl, phenyl-C₁₋₄alkyl-, C₁₋₄alkyl-oxy-C₁₋₄alkyl-; mono- or di(C₁₋₄alkyl)amino- or amino-carbonyl-;

Het¹⁴ represents a heterocycle selected from morpholinyl; pyrrolidinyl; piperazinyl; imidazolyl; pyrrolyl; 2,3,4-triazapyrrolyl; 1,2,3-triazolyl; pyrazolyl; or piperidinyl wherein said Het¹⁴ is optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-; in particular Het¹⁴ represents a heterocycle selected from morpholinyl; pyrrolidinyl; pyrrolyl; 2,3,4-triazapyrrolyl; piperazinyl or piperidinyl wherein said Het¹⁴ is optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-; more particular Het¹⁴ represents a heterocycle selected from morpholinyl; pyrrolidinyl; piperazinyl or piperidinyl wherein said Het¹⁴ is optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (1).

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (2).

3-{3-[(4-Pyridin-3-yl-1,3,5-triazin-2-yl)amino]phenyl}propanoic acid. Referred to herein as “Compound 1”.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (3).

2-{3-[(4-Pyridin-3-yl-1,3,5-triazin-2-yl)amino]phenyl}ethanol. Referred to herein as “Compound 2”.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (4).

1,1-Dimethylethyl {2-[3-({4-[2-(3-hydroxyprop-1-yn-1-yl)pyridin-4-yl]-1,3,5-triazin-2-yl}amino)phenyl]ethyl}carbamate. Referred to herein as “Compound 3”.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (5).

1,1-Dimethylethyl {4-[4-(4-{[3-(hydroxymethyl)phenyl]amino}-1,3,5-triazin-2-yl)pyridin-2-yl]butyl}carbamate. Referred to herein as “Compound 4”.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (6).

1,1-Dimethylethyl {3-[{[5-(2-{[3-bromo-5-(hydroxymethyl)phenyl]amino}pyrimidin-4-yl)-2-(methyloxy)phenyl]methyl}(methyl)amino]propyl}carbamate. Referred to herein as “Compound 5”.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (7).

4-{[3-(3-Fluorophenyl)-3H-[1,2,3]triazolo[4,5-d]pyrimidin-5-yl]amino}benzoic acid. Referred to herein as “Compound 6”.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (8).

2-Fluoro-5-[(3-phenyl-3H-[1,2,3]triazolo[4,5-d]pyrimidin-5-yl)amino]benzoic acid. Referred to herein as “Compound 7”.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (9).

N-{[3-(5-{[3-(2-Aminopyrimidin-4-yl)phenyl]amino}-3H-[1,2,3]triazolo[4,5-d]pyrimidin-3-yl)phenyl]methyl)}cyclopropanecarboxamide. Referred to herein as “Compound 8”.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (10).

4-[(1-Cyclohexyl-1H-pyrazolo[3,4-d]pyrimidin-6-yl)amino]-N-[3-(methyloxy)propyl]benzenesulfonamide. Referred to herein as “Compound 9”.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (11).

4-Chloro-2-[(6-{[3-(chloromethyl)-4-methoxyphenyl]amino}pyrimidin-4-yl)amino]phenol. Referred to herein as “Compound 10”.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (12).

4-{[4-(4-Methyl-3,4-dihydroquinoxalin-1(2H)-yl)pyrimidin-2-yl]amino}-N-(1-methylpiperidin-4-yl)benzamide. Referred to herein as “Compound 11”.

In one embodiment, the aniline-pyridinotriazine is a compound of the Formula (13).

N-(2-Methoxy-4-{[(3-methoxypropyl)amino]methyl}phenyl)-4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine. Referred to herein as “Compound 12”.

In one embodiment, the compound that is capable of differentiating pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage is a cyclic aniline-pyridinotriazine of the Formula (14):

The N-oxide forms, the pharmaceutically acceptable addition salts and the stereochemically isomeric forms thereof, wherein:

m represents an integer from 1 to 4; n represents an integer from 1 to 4; Z represents N or C;

Y represents-NR²—C₁₋₆alkyl-CO—NR⁴—, —C₁₋₄alkyl-NR⁹-C₁₋₄alkyl-, C₁₋₆alkyl-CO-Het¹⁰-, -Het¹¹-CO—C₁₋₆alkyl-, -Het¹²-C₁₋₆alkyl-, —CO-Het¹³-C₁₋₆alkyl-, —CO—NR¹⁰—C₁₋₆alkyl-, -Het¹-C₁₋₆alkyl-CO—NR⁵—, or -Het²-CO—NR⁶— wherein the —C₁₋₆alkyl-linker in —NR²—C¹⁻⁶alkyl-CO—NR⁴-or-Het¹-C₁₋₆alkyl-CO—NR⁵— is optionally substituted with one or where possible two or more substituents selected from hydroxy, methoxy, aminocarbonyl, halo, phenyl, indolyl, methylsulfide, thiol, hydroxyphenyl, cyanophenyl, amino and hydroxycarbonyl;

X¹ represents a direct bond, C₁₋₄alkyl, C₁₋₄alkyloxy-, C₁₋₄alkyl-CO—, C₂₋₄alkenyl, C₂₋₄alkynyl, or C₁₋₄alkyl-NR³—, wherein said C₁₋₄alkyl or C₂₋₄alkenyl is optionally substituted with one or where possible two or more halo substituents;

X² represents a direct bond, C₁₋₄alkyl, C₁₋₄alkyloxy-, C₁₋₄alkyl-CO—, C₂₋₄alkenyl, C₂₋₄alkynyl, or C₁₋₄alkyl-NR⁷—, wherein said C₁₋₄alkyl or C₂₋₄alkenyl is optionally substituted with one or where possible two or more halo substituents;

R¹ and R⁸ each independently represent hydrogen, Het¹⁴, cyano, halo, hydroxy, C₁₋₆alkoxy-, C₁₋₆alkyl-, mono- or di(C₁₋₄alkyl)amino-carbonyl-, mono- or di(C₁₋₄alkyl)amino-sulfonyl, C₁₋₆alkoxy-substituted with halo or R¹ represents C₁₋₆alkyl substituted with one or where possible two or more substituents selected from hydroxy or halo;

R² and R⁹ each independently represents hydrogen, C₁₋₄alkyl, C₂₋₄alkenyl, Het³, Het⁴-C₁₋₄alkyl-, Het⁵-C₁₋₄alkylcarbonyl-, mono- or di(C₁₋₄alkyl)amino-C₁₋₄alkyl-carbonyl- or phenyl optionally substituted with one or where possible two or more substituents selected from hydrogen, hydroxy, amino or C₁₋₄alkyloxy-;

R³ and R⁷ each independently represent hydrogen, C₁₋₄alkyl, Het⁶, Het⁷-C₁₋₄alkyl-, C₂₋₄alkenylcarbonyl-optionally substituted with Het⁸-C₁₋₄alkylaminocarbonyl-, C₂₋₄alkenylsulfonyl-, C₁₋₄lkyloxyC₁₋₄alkyl- or phenyl optionally substituted with one or where possible two or more substituents selected from hydrogen, hydroxy, amino or C₁₋₄alkyloxy-;

R4, R5, R6 and R¹⁰ each independently represent hydrogen or C₁₋₄alkyl optionally substituted with hydroxy, Het⁹ or C₁₋₄alkyloxy;

Het¹ and Het² each independently represent a heterocycle selected from pyrrolidinyl, piperidinyl, piperazinyl, pyridinyl, pyrimidinyl, pyrazinyl, imidazolidinyl or pyrazolidinyl wherein said Het¹ and Het² are optionally substituted with amino, hydroxy, C₁₋₄alkyl, hydroxy-C₁₋₄alIcyl-, phenyl, phenyl-C₁₋₄alkyl-, C₁₋₄alkyl-oxy-C₁₋₄alkyl-mono- or di(C₁₋₄alkyl) amino- or amino-carbonyl-;

Het³ and Het⁶ each independently represent, heterocycle selected from pyrrolidinyl or piperidinyl wherein said Het³ and Het⁶ are optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-;

Het⁴, Het⁷ and Het⁹ each independently represent a heterocycle selected from morpholinyl, pyrrolidinyl, piperazinyl or piperidinyl wherein said Het⁴, Het⁷ and Het⁹ are optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-;

Het⁵ represents a heterocycle selected from morpholinyl, pyrrolidinyl, piperazinyl or pipendinyl wherein said Het⁵ is optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-;

Het¹⁰, Het¹¹ and Het¹³ each independently represent a heterocycle selected from pyrrolidinyl, piperidinyl, piperazinyl, pyridinyl, pyrimidinyl, pyrazinyl, imidazolidinyl or pyrazolidinyl wherein said Het¹⁰, Het¹¹ and Het¹³ are optionally substituted with amino, hydroxy, C₁₋₄alkyl, hydroxy-C₁₋₄alkyl-, phenyl, phenyl-C₁₋₄alkyl-, C₁₋₄alkyl-oxy-C₁₋₄alkyl-, amino-carbonyl- or mono- or di(C₁₋₄alkyl)amino-;

Het¹² represents a heterocycle selected from pyrrolidinyl, piperidinyl, piperazinyl, pyridinyl, pyrimidinyl, pyrazinyl, imidazolidinyl or pyrazolidinyl wherein said Het¹² is optionally substituted with amino, hydroxy, C₁₋₄alkyl, hydroxy-C₁₋₄alkyl-, phenyl, phenyl-C₁₋₄alkyl-, C₁₋₄alkyl-oxy-C₁₋₄alkyl-; mono- or di(C₁₋₄alkyl)amino- or amino-carbonyl-;

Het¹⁴ represents a heterocycle selected from morpholinyl; pyrrolidinyl; piperazinyl; imidazolyl; pyrrolyl; 2,3,4-triazapyrrolyl; 1,2,3-triazolyl; pyrazolyl; or piperidinyl wherein said Het¹⁴ is optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-; in particular Het¹⁴ represents a heterocycle selected from morpholinyl; pyrrolidinyl; pyrrolyl; 2,3,4-triazapyrrolyl; piperazinyl or piperidinyl wherein said Het¹⁴ is optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-; more particular Het¹⁴ represents a heterocycle selected from morpholinyl; pyrrolidinyl; piperazinyl or piperidinyl wherein said Het¹⁴ is optionally substituted with one or where possible two or more substituents selected from C₁₋₄alkyl, C₃₋₆cycloalkyl, hydroxy-C₁₋₄alkyl-, C₁₋₄alkyloxyC₁₋₄alkyl or polyhydroxy-C₁₋₄alkyl-.

Compounds of Formula (7) are disclosed in WO2007/003525, assigned to Janssen Pharmaceutica N.V.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (14).

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (15).

1,8,10,12,17,19,23,27,33-Nonaazapentacyclo[25.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜]tetratriaconta-3(34),4,6,9(33),10,12,14(32),15,17-nonaen-24-one. Referred to herein as “Compound 13”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (16).

10-Chloro-14-ethyl-3,5,7,14,17,22,27-heptaazatetracyclo[19.3.1.1˜2,6˜.1˜8,12˜]heptacosa-1(25),2(27),3,5,8(26),9,11,21,23-nonaen-16-one. Referred to herein as “Compound 14”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (17).

14-Ethyl-3,5,7,14,17,27-hexaazatetracyclo[19.3.1.1˜2,6˜.1˜8,12˜]heptacosa-1(25),2(27),3,5,8(26),9,11,21,23-nonaen-16-one. Referred to herein as “Compound 15”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (18).

10-Chloro-14-ethyl-3,5,7,14,17,27-hexaazatetracyclo[19.3.1.1˜2,6˜.1˜8,12˜]heptacosa-1(25),2(27),3,5,8(26),9,11,21,23-nonaen-16-one. Referred to herein as “Compound 16”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (19).

3,5,7,14,20,26,31-Heptaazapentacyclo[22.3.1.1˜2,6˜.1˜8,12˜.1˜14,18˜]hentriaconta-1(28),2(31),3,5,8(30),9,11,24,26-nonaen-19-one. Referred to herein as “Compound 17”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (20).

(18S)-3,5,7,14,20,26,30-Heptaazapentacyclo[22.3.1.1˜2,6˜.1˜8,12˜.0˜14,18˜]triaconta-1(28),2(30),3,5,8(29),9,11,24,26-nonaen-19-one. Referred to herein as “Compound 18”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (21).

14-Methyl-3,5,7,14,18,24,28-heptaazatetracyclo[20.3.1.1˜2,6˜.1˜8,12˜]octacosa-1(26),2(28),3,5,8(27),9,11,22,24-nonaen-17-one. Referred to herein as “Compound 19”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (22).

14-Methyl-3,5,7,14,19,25,29-heptaazatetracyclo[21.3.1.1˜2,6˜.1˜8,12˜]nonacosa-1(27),2(29),3,5,8(28),9,11,23,25-nonaen-18-one. Referred to herein as “Compound 20”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (23).

14-Methyl-3,5,7,14,18,22,29-heptaazatetracyclo[21.3.1.1˜2,6˜.1˜8,12˜]nonacosa-1(27),2(29),3,5,8(28),9,11,23,25-nonaen-17-one. Referred to herein as “Compound 21”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (24).

1,8,10,12,16,22,30-Heptaazapentacyclo[22.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜]hentriaconta-3(31),4,6,9(30),10,12,14(29),15,17-nonaen-23-one. Referred to herein as “Compound 22”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (25).

1,8,10,12,16,22,26,32-Octaazapentacyclo[24.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜]tritriaconta-3(33),4,6,9(32),10,12,14(31),15,17-nonaen-23-one. Referred to herein as “Compound 23”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (26).

5-Chloro-17-fluoro-1,8,10,12,22,26,32-heptaazapentacyclo[24.2.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜]tritriaconta-3(33),4,6,9(32),10,12,14(31),15,17-nonaen-23-one. Referred to herein as “Compound 24”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (27).

10-Chloro-14-ethyl-22-fluoro-3,5,7,14,17,27-hexaazatetracyclo[19.3.1.1˜2,6˜.1˜8,12˜]heptacosa-1(25),2(27),3,5,8(26),9,11,21,23-nonaen-16-one. Referred to herein as “Compound 25”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (28).

10-Chloro-25-fluoro-3,5,7,14,20,31-hexaazapentacyclo[22.3.1.1˜2,6˜.1˜8,12˜.1˜14,18˜]hentriaconta-1(28),2(31),3,5,8(30),9,11,24,26-nonaen-19-one. Referred to herein as “Compound 26”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (29).

4-Chloro-1,8,10,12,17,22,26,32-octaazapentacyclo[24.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜]tritriaconta-3(33),4,6,9(32),10,12,14(31),15,17-nonaen-23-one. Referred to herein as “Compound 27”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (30).

18-Methyl-3,5,7,15,18,28-hexaazatetracyclo[20.3.1.1˜2,6˜.1˜8,12˜]octacosa-1(26),2(28),3,5,8(27),9,11,22,24-nonaen-16-one. Referred to herein as “Compound 28”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (31).

18-Ethyl-3,5,7,15,18,28-hexaazatetracyclo[20.3.1.1˜2,6˜.1˜8,12˜]octacosa-1(26),2(28),3,5,8(27),9,11,22,24-nonaen-16-one. Referred to herein as “Compound 29”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (32).

1,8,10,12,17,19,23,27,33-Nonaazapentacyclo[25.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜]tetratriaconta-3(34),4,6,9(33),10,12,14(32),15,17-nonaen-24-one. Referred to herein as “Compound 30”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (33).

1,11,13,15,23,31-Hexaazapentacyclo[23.2.2.1˜5,9˜.1˜10,14˜.1˜16,20˜]dotriaconta-5(32),6,8,10(31),11,13,16(30),17,19-nonaen-24-one. Referred to herein as “Compound 31”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (34).

15-Ethyl-13,14,15,16,18,19-hexahydro-1H-6,2-(azeno)-7,11-(metheno)-1,3,5,15,18-benzopentaazacyclohenicosin-17(12H)-one. Referred to herein as “Compound 32”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (35).

20-Methyl-3,5,7,15,20,30-hexaazatetracyclo[22.3.1.1˜2,6˜.1˜8,12˜]triaconta-1(28),2(30),3,5,8(29),9,11,24,26-nonaen-16-one. Referred to herein as “Compound 33”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (36).

5-Chloro-1,8,10,12,16,22,26,32-octaazapentacyclo[24.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜]tritriaconta-3(33),4,6,9(32),10,12,14(31),15,17-nonaen-23-one. Referred to herein as “Compound 34”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (37).

10-Chloro-14-ethyl-3,5,7,14,17,23,27-heptaazatetracyclo[19.3.1.1˜2,6˜.1˜8,12˜]heptacosa-1(25),2(27),3,5,8(26),9,11,21,23-nonaen-16-one. Referred to herein as “Compound 35”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (38).

(18S)-10-Chloro-3,5,7,14,20,26,30-heptaazapentacyclo[22.3.1.1˜2,6˜.1˜8,12˜.0˜14,18˜]triaconta-1(28),2(30),3,5,8(29),9,11,24,26-nonaen-19-one. Referred to herein as “Compound 36”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (39).

10-Chloro-3,5,7,14,20,26,31-heptaazapentacyclo[22.3.1.1˜2,6˜.1˜8,12˜.1˜14,18˜]hentriaconta-1(28),2(31),3,5,8(30),9,11,24,26-nonaen-19-one. Referred to herein as “Compound 37”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (40).

5-Chloro-1,8,10,12,16,22,30-heptaazapentacyclo[22.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜]hentriaconta-3(31),4,6,9(30),10,12,14(29),15,17-nonaen-23-one. Referred to herein as “Compound 38”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (41).

9-Methyl-2,3,4,5,7,8,9,10-octahydro-16H-17,21-(azeno)-11,15-(metheno)pyrido[3,2-g][1,3,5,9,13,17]hexaazacyclotricosin-6(1H)-one. Referred to herein as “Compound 39”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (42).

14-Prop-2-en-1-yl-3,5,7,14,17,23,27-heptaazatetracyclo[19.3.1.1˜2,6˜.1˜8,12˜]heptacosa-1(25),2(27),3,5,8(26),9,11,21,23-nonaen-16-one. Referred to herein as “Compound 40”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (43).

18-Oxo-14-oxa-2,4,8,17,25-pentaazatetracyclo[17.3.1.1˜3,7˜.1˜9,13˜]pentacosa-1(23),3(25),4,6,9(24),10,12,19,21-nonaene-6-carbonitrile. Referred to herein as “Compound 41”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (44).

14,21-Dioxa-2,4,8,18,28-pentaazatetracyclo[20.3.1.1˜3,7˜.1˜9,13˜]octacosa-1(26),3(28),4,6,9(27),10,12,22,24-nonaen-19-one. Referred to herein as “Compound 42”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (45).

21-Methyl-1,8,10,11,21,24,30-heptaazapentacyclo[22.2.2.1˜3,7˜.1˜9,12˜.1˜13,17˜]hentriaconta-3(31),4,6,9,11,13(29),14,16-octaen-23-one. Referred to herein as “Compound 43”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (46).

(18S)-11-(Morpholin-4-ylcarbonyl)-5,7,14,20,28-pentaazapentacyclo[20.3.1.1˜2,6˜.1˜8,12˜.0˜14,18˜]octacosa-1(26),2(28),3,5,8(27),9,11,22,24-nonaen-19-one. Referred to herein as “Compound 44”.

In one embodiment, the cyclic aniline-pyridinotriazine is a compound of the Formula (47).

10-Methoxy-17-methyl-2,14,15,17,18,19,20,22-octahydro-6H-19,21-methano-7,11-(metheno)-12-oxa-2,3,5,6,17,21-hexaazacycloicosa[1,2,3-cd]inden-16(13H)-one. Referred to herein as “Compound 45”.

In one embodiment, the at least one other factor is a compound of the Formula (48):

N-{[1-(Phenylmethyl)azepan-4-yl]methyl}-2-pyridin-3-ylacetamide. Referred herein as “Compound 46”.

In one embodiment, the at least one other factor is a compound of the Formula (49):

4-{[4-(4-{[2-(Pyridin-2-ylamino)ethyl]amino}-1,3,5-triazin-2-yl)pyridin-2-yl]oxy}butan-1-ol. Referred herein as “Compound 47”.

In one embodiment, the at least one other factor is a compound of the Formula (50):

3-({3-[4-({2-[Methyl(pyridin-2-yl)amino]ethyl}amino)-1,3,5-triazin-2-yl]pyridin-2-yl}amino)propan-1-ol. Referred herein as “Compound 48”.

In one embodiment, the at least one other factor is a compound of the Formula (51):

N˜4˜-[2-(3-Fluorophenyl)ethyl]-N˜2˜-[3-(4-methylpiperazin-1-yl)propyl]pyrido[2,3-d]pyrimidine-2,4-diamine. Referred herein as “Compound 49”.

In one embodiment, the at least one other factor is a compound of the Formula (52):

1-Methyl-N-[(4-pyridin-3-yl-2-{[3-(trifluoromethyl)phenyl]amino}-1,3-thiazol-5-yl)methyl]piperidine-4-carboxamide. Referred herein as “Compound 50”.

In one embodiment, the at least one other factor is a compound of the Formula (53):

1,1-Dimethylethyl {2-[4-({5-[3-(3-hydroxypropyl)phenyl]-4H-1,2,4-triazol-3-yl}amino)phenyl]ethyl}carbamate. Referred herein as “Compound 51”.

In one embodiment, the at least one other factor is a compound of the Formula (54):

1,1-Dimethylethyl {[3-({5-[5-(3-hydroxypropyl)-2-(methyloxy)phenyl]-1,3-oxazol-2-yl}amino)phenyl]methyl}carbamate. Referred herein as “Compound 52”.

In one embodiment, the at least one other factor is a compound of the Formula (55):

1-({5-[6-({4-[(4-Methylpiperazin-1-yl)sulfonyl]phenyl}amino)pyrazin-2-yl]thiophen-2-yl}methyl)piperidin-4-ol. Referred herein as “Compound 53”.

In one embodiment, the at least one other factor is a compound of the Formula (56):

1-({4-[6-({4-[(4-Methylpiperazin-1-yl)sulfonyl]phenyl}amino)pyrazin-2-yl]thiophen-2-yl}methyl)piperidine-4-carboxamide. Referred herein as “Compound 54”.

In one embodiment, the at least one other factor is a compound of the Formula (57):

2-{[4-(1-Methylethyl)phenyl]amino}-N-(2-thiophen-2-ylethyl)-7,8-dihydropyrido[4,3-d]pyrimidine-6(5H)-carboxamide. Referred herein as “Compound 55”.

In one embodiment, the at least one other factor is a compound of the Formula (58):

6-[(2-{[4-(2,4-Dichlorophenyl)-5-(4-methyl-1H-imidazol-2-yl)pyrimidin-2-yl]amino}ethyl)amino]pyridine-3-carbonitrile. Referred herein as “Compound 56”.

In one embodiment, the at least one other factor is a compound of the Formula (59):

4-(6-{[(3-Chlorophenyl)methyl]amino}imidazo[1,2-b]pyridazin-3-yl)-N-[2-(dimethylamino)ethyl]benzamide. Referred herein as “Compound 57”.

Detection of Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage

Formation of cells expressing markers characteristic of the definitive endoderm lineage may be determined by testing for the presence of the markers before and after following a particular protocol. Pluripotent stem cells typically do not express such markers. Thus, differentiation of pluripotent cells is detected when cells begin to express them.

The efficiency of differentiation may be determined by exposing a treated cell population to an agent (such as an antibody) that specifically recognizes a protein marker expressed by cells expressing markers characteristic of the definitive endoderm lineage.

Methods for assessing expression of protein and nucleic acid markers in cultured or isolated cells are standard in the art. These include quantitative reverse transcriptase polymerase chain reaction (RT-PCR), Northern blots, in situ hybridization (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 2001 supplement)), and immunoassays such as immunohistochemical analysis of sectioned material, Western blotting, and for markers that are accessible in intact cells, flow cytometry analysis (FACS) (see, e.g., Harlow and Lane, Using Antibodies: A Laboratory Manual, New York: Cold Spring Harbor Laboratory Press (1998)).

For example, characteristics of pluripotent stem cells are well known to those skilled in the art, and additional characteristics of pluripotent stem cells continue to be identified. Pluripotent stem cell markers include, for example, the expression of one or more of the following: ABCG2, cripto, FOXD3, Connexin43, Connexin45, OCT4, SOX2, Nanog, hTERT, UTF-1, ZFP42, SSEA-3, SSEA-4, Tra1-60, or Tra1-81.

After treating pluripotent stem cells with the methods of the present invention, the differentiated cells may be purified by exposing a treated cell population to an agent (such as an antibody) that specifically recognizes a protein marker, such as CXCR4, expressed by cells expressing markers characteristic of the definitive endoderm lineage.

Formation of Cells Expressing Markers Characteristic of the Pancreatic Endoderm Lineage

Cells expressing markers characteristic of the definitive endoderm lineage may be differentiated into cells expressing markers characteristic of the pancreatic endoderm lineage by any method in the art or by any method proposed in this invention.

For example, cells expressing markers characteristic of the definitive endoderm lineage may be differentiated into cells expressing markers characteristic of the pancreatic endoderm lineage according to the methods disclosed in D'Amour et al., Nature Biotechnology 24, 1392-1401 (2006).

For example, cells expressing markers characteristic of the definitive endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endoderm lineage, by treating the cells expressing markers characteristic of the definitive endoderm lineage with a fibroblast growth factor and the hedgehog signaling pathway inhibitor KAAD-cyclopamine, then removing the medium containing the fibroblast growth factor and KAAD-cyclopamine and subsequently culturing the cells in medium containing retinoic acid, a fibroblast growth factor and KAAD-cyclopamine. An example of this method is disclosed in Nature Biotechnology 24, 1392-1401 (2006).

In one aspect of the present invention, cells expressing markers characteristic of the definitive endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endoderm lineage, by treating the cells expressing markers characteristic of the definitive endoderm lineage with retinoic acid and at least one fibroblast growth factor for a period of time, according to the methods disclosed in U.S. patent application Ser. No. 11/736,908, assigned to LifeScan, Inc.

In one aspect of the present invention, cells expressing markers characteristic of the definitive endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endoderm lineage, by treating the cells expressing markers characteristic of the definitive endoderm lineage with retinoic acid and at least one fibroblast growth factor for a period of time, according to the methods disclosed in U.S. patent application Ser. No. 11/779,311, assigned to LifeScan, Inc.

In one aspect of the present invention, cells expressing markers characteristic of the definitive endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endoderm lineage, by treating the cells expressing markers characteristic of the definitive endoderm lineage according to the methods disclosed in U.S. patent application Ser. No. 60/990,529.

Cells expressing markers characteristic of the definitive endoderm lineage may be treated with at least one other additional factor that may enhance the formation of cells expressing markers characteristic of the pancreatic endoderm lineage. Alternatively, the at least one other additional factor may enhance the proliferation of the cells expressing markers characteristic of the pancreatic endoderm lineage formed by the methods of the present invention. Further, the at least one other additional factor may enhance the ability of the cells expressing markers characteristic of the pancreatic endoderm lineage formed by the methods of the present invention to form other cell types, or improve the efficiency of any other additional differentiation steps.

The at least one additional factor may be, for example, nicotinamide, members of TGF-β family, including TGF-β1, 2, and 3, serum albumin, members of the fibroblast growth factor family, platelet-derived growth factor-AA, and -BB, platelet rich plasma, insulin growth factor (IGF-I, II), growth differentiation factor (such as, for example, GDF-5, -6, -8, -10, -11), glucagon like peptide-I and II (GLP-I and II), GLP-1 and GLP-2 mimetobody, Exendin-4, retinoic acid, parathyroid hormone, insulin, progesterone, aprotinin, hydrocortisone, ethanolamine, beta mercaptoethanol, epidermal growth factor (EGF), gastrin I and II, copper chelators such as, for example, triethylene pentamine, forskolin, Na-Butyrate, activin, betacellulin, ITS, noggin, neurite growth factor, nodal, valproic acid, trichostatin A, sodium butyrate, hepatocyte growth factor (HGF), sphingosine-1, VEGF, MG132 (EMD, CA), N2 and B27 supplements (Gibco, CA), steroid alkaloid such as, for example, cyclopamine (EMD, CA), keratinocyte growth factor (KGF), Dickkopf protein family, bovine pituitary extract, islet neogenesis-associated protein (INGAP), Indian hedgehog, sonic hedgehog, proteasome inhibitors, notch pathway inhibitors, sonic hedgehog inhibitors, or combinations thereof.

The at least one other additional factor may be supplied by conditioned media obtained from pancreatic cells lines such as, for example, PANC-1 (ATCC No: CRL-1469), CAPAN-1 (ATCC No: HTB-79), BxPC-3 (ATCC No: CRL-1687), HPAF-II (ATCC No: CRL-1997), hepatic cell lines such as, for example, HepG2 (ATCC No: HTB-8065), and intestinal cell lines such as, for example, FHs 74 (ATCC No: CCL-241).

Detection of Cells Expressing Markers Characteristic of the Pancreatic Endoderm Lineage

Markers characteristic of the pancreatic endoderm lineage are well known to those skilled in the art, and additional markers characteristic of the pancreatic endoderm lineage continue to be identified. These markers can be used to confirm that the cells treated in accordance with the present invention have differentiated to acquire the properties characteristic of the pancreatic endoderm lineage. Pancreatic endoderm lineage specific markers include the expression of one or more transcription factors such as, for example, Hlxb9, PTF-1a, PDX-1, HNF-6, HNF-1beta.

The efficiency of differentiation may be determined by exposing a treated cell population to an agent (such as an antibody) that specifically recognizes a protein marker expressed by cells expressing markers characteristic of the pancreatic endoderm lineage.

Methods for assessing expression of protein and nucleic acid markers in cultured or isolated cells are standard in the art. These include quantitative reverse transcriptase polymerase chain reaction (RT-PCR), Northern blots, in situ hybridization (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 2001 supplement)), and immunoassays such as immunohistochemical analysis of sectioned material, Western blotting, and for markers that are accessible in intact cells, flow cytometry analysis (FACS) (see, e.g., Harlow and Lane, Using Antibodies: A Laboratory Manual, New York: Cold Spring Harbor Laboratory Press (1998)).

Formation of Cells Expressing Markers of the Pancreatic Endocrine Lineage

Cells expressing markers characteristic of the pancreatic endoderm lineage may be differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage by any method in the art or by any method disclosed in this invention.

For example, cells expressing markers characteristic of the pancreatic endoderm lineage may be differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage according to the methods disclosed in D'Amour et al., Nature Biotechnology 24, 1392-1401 (2006).

For example, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by culturing the cells expressing markers characteristic of the pancreatic endoderm lineage in medium containing DAPT and exendin 4, then removing the medium containing DAPT and exendin 4 and subsequently culturing the cells in medium containing exendin 1, IGF-1 and HGF. An example of this method is disclosed in Nature Biotechnology 24, 1392-1401 (2006).

For example, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by culturing the cells expressing markers characteristic of the pancreatic endoderm lineage in medium containing exendin 4, then removing the medium containing exendin 4 and subsequently culturing the cells in medium containing exendin 1, IGF-1 and HGF. An example of this method is disclosed in D'Amour et al., Nature Biotechnology, 2006.

For example, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by culturing the cells expressing markers characteristic of the pancreatic endoderm lineage in medium containing DAPT and exendin 4. An example of this method is disclosed in D'Amour et al., Nature Biotechnology, 2006.

For example, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by culturing the cells expressing markers characteristic of the pancreatic endoderm lineage in medium containing exendin 4. An example of this method is disclosed in D' Amour et al., Nature Biotechnology, 2006.

In one aspect of the present invention, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by treating the cells expressing markers characteristic of the pancreatic endoderm lineage with a factor that inhibits the Notch signaling pathway, according to the methods disclosed in U.S. patent application Ser. No. 11/736,908, assigned to LifeScan, Inc.

In one aspect of the present invention, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by treating the cells expressing markers characteristic of the pancreatic endoderm lineage with a factor that inhibits the Notch signaling pathway, according to the methods disclosed in U.S. patent application Ser. No. 11/779,311, assigned to LifeScan, Inc.

In one aspect of the present invention, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by treating the cells expressing markers characteristic of the pancreatic endoderm lineage with a factor that inhibits the Notch signaling pathway, according to the methods disclosed in U.S. patent application Ser. No. 60/953,178, assigned to LifeScan, Inc.

In one aspect of the present invention, cells expressing markers characteristic of the pancreatic endoderm lineage are further differentiated into cells expressing markers characteristic of the pancreatic endocrine lineage, by treating the cells expressing markers characteristic of the pancreatic endoderm lineage according to the methods disclosed in U.S. patent application Ser. No. 60/990,529.

Cells expressing markers characteristic of the pancreatic endoderm lineage may be treated with at least one other additional factor that may enhance the formation of cells expressing markers characteristic of the pancreatic endocrine lineage. Alternatively, the at least one other additional factor may enhance the proliferation of the cells expressing markers characteristic of the pancreatic endocrine lineage formed by the methods of the present invention. Further, the at least one other additional factor may enhance the ability of the cells expressing markers characteristic of the pancreatic endocrine lineage formed by the methods of the present invention to form other cell types or improve the efficiency of any other additional differentiation steps.

The at least one additional factor may be, for example, nicotinamide, members of TGF-β family, including TGF-β1, 2, and 3, serum albumin, members of the fibroblast growth factor family, platelet-derived growth factor-AA, and -BB, platelet rich plasma, insulin growth factor (IGF-I, II), growth differentiation factor (such as, for example, GDF-5, -6, -8, -10, -11), glucagon like peptide-I and II (GLP-I and II), GLP-1 and GLP-2 mimetobody, Exendin-4, retinoic acid, parathyroid hormone, insulin, progesterone, aprotinin, hydrocortisone, ethanolamine, beta mercaptoethanol, epidermal growth factor (EGF), gastrin I and II, copper chelators such as, for example, triethylene pentamine, forskolin, Na-Butyrate, activin, betacellulin, ITS, noggin, neurite growth factor, nodal, valproic acid, trichostatin A, sodium butyrate, hepatocyte growth factor (HGF), sphingosine-1, VEGF, MG132 (EMD, CA), N2 and B27 supplements (Gibco, CA), steroid alkaloid such as, for example, cyclopamine (EMD, CA), keratinocyte growth factor (KGF), Dickkopf protein family, bovine pituitary extract, islet neogenesis-associated protein (INGAP), Indian hedgehog, sonic hedgehog, proteasome inhibitors, notch pathway inhibitors, sonic hedgehog inhibitors, or combinations thereof.

The at least one other additional factor may be supplied by conditioned media obtained from pancreatic cells lines such as, for example, PANC-1 (ATCC No: CRL-1469), CAPAN-1 (ATCC No: HTB-79), BxPC-3 (ATCC No: CRL-1687), HPAF-II (ATCC No: CRL-1997), hepatic cell lines such as, for example, HepG2 (ATCC No: HTB-8065), and intestinal cell lines such as, for example, FHs 74 (ATCC No: CCL-241).

Detection of Cells Expressing Markers Characteristic of the Pancreatic Endocrine Lineage

Markers characteristic of cells of the pancreatic endocrine lineage are well known to those skilled in the art, and additional markers characteristic of the pancreatic endocrine lineage continue to be identified. These markers can be used to confirm that the cells treated in accordance with the present invention have differentiated to acquire the properties characteristic of the pancreatic endocrine lineage. Pancreatic endocrine lineage specific markers include the expression of one or more transcription factors such as, for example, NGN3, NEURO, or ISL1.

Markers characteristic of cells of the β cell lineage are well known to those skilled in the art, and additional markers characteristic of the β cell lineage continue to be identified. These markers can be used to confirm that the cells treated in accordance with the present invention have differentiated to acquire the properties characteristic of the β-cell lineage. β cell lineage specific characteristics include the expression of one or more transcription factors such as, for example, PDX1, NKX2.2, NKX6.1, ISL1, PAX6, PAX4, NEUROD, HNF1 beta, HNF6, HNF3 beta, or MAFA, among others. These transcription factors are well established in the art for identification of endocrine cells. See, e.g., Edlund (Nature Reviews Genetics 3: 524-632 (2002)).

The efficiency of differentiation may be determined by exposing a treated cell population to an agent (such as an antibody) that specifically recognizes a protein marker expressed by cells expressing markers characteristic of the pancreatic endocrine lineage. Alternatively, the efficiency of differentiation may be determined by exposing a treated cell population to an agent (such as an antibody) that specifically recognizes a protein marker expressed by cells expressing markers characteristic of the β cell lineage.

Methods for assessing expression of protein and nucleic acid markers in cultured or isolated cells are standard in the art. These include quantitative reverse transcriptase polymerase chain reaction (RT-PCR), Northern blots, in situ hybridization (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 2001 supplement)), and immunoassays such as immunohistochemical analysis of sectioned material, Western blotting, and for markers that are accessible in intact cells, flow cytometry analysis (FACS) (see, e.g., Harlow and Lane, Using Antibodies: A Laboratory Manual, New York: Cold Spring Harbor Laboratory Press (1998)).

In one aspect of the present invention, the efficiency of differentiation is determined by measuring the percentage of insulin positive cells in a given cell culture following treatment. In one embodiment, the methods of the present invention produce about 100% insulin positive cells in a given culture. In an alternate embodiment, the methods of the present invention produce about 90% insulin positive cells in a given culture. In an alternate embodiment, the methods of the present invention produce about 80% insulin positive cells in a given culture. In an alternate embodiment, the methods of the present invention produce about 70% insulin positive cells in a given culture. In an alternate embodiment, the methods of the present invention produce about 60% insulin positive cells in a given culture. In an alternate embodiment, the methods of the present invention produce about 50% insulin positive cells in a given culture. In an alternate embodiment, the methods of the present invention produce about 40% insulin positive cells in a given culture. In an alternate embodiment, the methods of the present invention produce about 30% insulin positive cells in a given culture. In an alternate embodiment, the methods of the present invention produce about 20% insulin positive cells in a given culture. In an alternate embodiment, the methods of the present invention produce about 10% insulin positive cells in a given culture. In an alternate embodiment, the methods of the present invention produce about 5% insulin positive cells in a given culture.

In one aspect of the present invention, the efficiency of differentiation is determined by measuring glucose-stimulated insulin secretion, as detected by measuring the amount of C-peptide released by the cells. In one embodiment, cells produced by the methods of the present invention produce about 1000 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 900 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 800 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 700 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 600 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 500 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 400 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 500 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 400 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 300 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 200 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 100 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 90 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 80 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 70 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 60 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 50 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 40 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 30 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 20 ng C-peptide/pg DNA. In an alternate embodiment, cells produced by the methods of the present invention produce about 10 ng C-peptide/pg DNA.

Therapies

In one aspect, the present invention provides a method for treating a patient suffering from, or at risk of developing, Type1 diabetes. This method involves culturing pluripotent stem cells, differentiating the pluripotent stem cells in vitro into a β-cell lineage, and implanting the cells of a β-cell lineage into a patient.

In yet another aspect, this invention provides a method for treating a patient suffering from, or at risk of developing, Type 2 diabetes. This method involves culturing pluripotent stem cells, differentiating the cultured cells in vitro into a β-cell lineage, and implanting the cells of a β-cell lineage into the patient.

If appropriate, the patient can be further treated with pharmaceutical agents or bioactives that facilitate the survival and function of the transplanted cells. These agents may include, for example, insulin, members of the TGF-β family, including TGF-β1, 2, and 3, bone morphogenic proteins (BMP-2, -3, -4, -5, -6, -7, -11, -12, and -13), fibroblast growth factors-1 and -2, platelet-derived growth factor-AA, and —BB, platelet rich plasma, insulin growth factor (IGF-I, II) growth differentiation factor (such as, for example, GDF-5, -6, -7, -8, -10, -15), vascular endothelial cell-derived growth factor (VEGF), pleiotrophin, endothelin, among others. Other pharmaceutical compounds can include, for example, nicotinamide, glucagon like peptide-I (GLP-1) and II, GLP-1 and -2 mimetibody, Exendin-4, retinoic acid, parathyroid hormone, MAPK inhibitors, such as, for example, compounds disclosed in U.S. Published Application 2004/0209901 and U.S. Published Application 2004/0132729.

The pluripotent stem cells may be differentiated into an insulin-producing cell prior to transplantation into a recipient. In a specific embodiment, the pluripotent stem cells are fully differentiated into β-cells prior to transplantation into a recipient. Alternatively, the pluripotent stem cells may be transplanted into a recipient in an undifferentiated or partially differentiated state. Further differentiation may take place in the recipient.

Definitive endoderm cells or, alternatively, pancreatic endoderm cells, or, alternatively, β cells, may be implanted as dispersed cells or formed into clusters that may be infused into the hepatic portal vein. Alternatively, cells may be provided in biocompatible degradable polymeric supports, porous non-degradable devices or encapsulated to protect from host immune response. Cells may be implanted into an appropriate site in a recipient. The implantation sites include, for example, the liver, natural pancreas, renal subcapsular space, omentum, peritoneum, subserosal space, intestine, stomach, or a subcutaneous pocket.

To enhance further differentiation, survival or activity of the implanted cells, additional factors, such as growth factors, antioxidants or anti-inflammatory agents, can be administered before, simultaneously with, or after the administration of the cells. In certain embodiments, growth factors are utilized to differentiate the administered cells in vivo. These factors can be secreted by endogenous cells and exposed to the administered cells in situ. Implanted cells can be induced to differentiate by any combination of endogenous and exogenously administered growth factors known in the art.

The amount of cells used in implantation depends on a number of various factors including the patient's condition and response to the therapy, and can be determined by one skilled in the art.

In one aspect, this invention provides a method for treating a patient suffering from, or at risk of developing diabetes. This method involves culturing pluripotent stem cells, differentiating the cultured cells in vitro into a β-cell lineage, and incorporating the cells into a three-dimensional support. The cells can be maintained in vitro on this support prior to implantation into the patient. Alternatively, the support containing the cells can be directly implanted in the patient without additional in vitro culturing. The support can optionally be incorporated with at least one pharmaceutical agent that facilitates the survival and function of the transplanted cells.

Support materials suitable for use for purposes of the present invention include tissue templates, conduits, barriers, and reservoirs useful for tissue repair. In particular, synthetic and natural materials in the form of foams, sponges, gels, hydrogels, textiles, and nonwoven structures, which have been used in vitro and in vivo to reconstruct or regenerate biological tissue, as well as to deliver chemotactic agents for inducing tissue growth, are suitable for use in practicing the methods of the present invention. See, for example, the materials disclosed in U.S. Pat. Nos. 5,770,417, 6,022,743, 5,567,612, 5,759,830, 6,626,950, 6,534,084, 6,306,424, 6,365,149, 6,599,323, 6,656,488, U.S. Published Application 2004/0062753 A1, U.S. Pat. Nos. 4,557,264 and 6,333,029.

To form a support incorporated with a pharmaceutical agent, the pharmaceutical agent can be mixed with the polymer solution prior to forming the support. Alternatively, a pharmaceutical agent could be coated onto a fabricated support, preferably in the presence of a pharmaceutical carrier. The pharmaceutical agent may be present as a liquid, a finely divided solid, or any other appropriate physical form. Alternatively, excipients may be added to the support to alter the release rate of the pharmaceutical agent. In an alternate embodiment, the support is incorporated with at least one pharmaceutical compound that is an anti-inflammatory compound, such as, for example, compounds disclosed in U.S. Pat. No. 6,509,369.

The support may be incorporated with at least one pharmaceutical compound that is an anti-apoptotic compound, such as, for example, compounds disclosed in U.S. Pat. No. 6,793,945.

The support may also be incorporated with at least one pharmaceutical compound that is an inhibitor of fibrosis, such as, for example, compounds disclosed in U.S. Pat. No. 6,331,298.

The support may also be incorporated with at least one pharmaceutical compound that is capable of enhancing angiogenesis, such as, for example, compounds disclosed in U.S. Published Application 2004/0220393 and U.S. Published Application 2004/0209901.

The support may also be incorporated with at least one pharmaceutical compound that is an immunosuppressive compound, such as, for example, compounds disclosed in U.S. Published Application 2004/0171623.

The support may also be incorporated with at least one pharmaceutical compound that is a growth factor, such as, for example, members of the TGF-β family, including TGF-β1, 2, and 3, bone morphogenic proteins (BMP-2, -3, -4, -5, -6, -7, -11, -12, and -13), fibroblast growth factors-1 and -2, platelet-derived growth factor-AA, and -BB, platelet rich plasma, insulin growth factor (IGF-I, II) growth differentiation factor (such as, for example, GDF-5, -6, -8, -10, -15), vascular endothelial cell-derived growth factor (VEGF), pleiotrophin, endothelin, among others. Other pharmaceutical compounds can include, for example, nicotinamide, hypoxia inducible factor 1-alpha, glucagon like peptide-I (GLP-1), GLP-1 and GLP-2 mimetibody, and II, Exendin-4, nodal, noggin, NGF, retinoic acid, parathyroid hormone, tenascin-C, tropoelastin, thrombin-derived peptides, cathelicidins, defensins, laminin, biological peptides containing cell- and heparin-binding domains of adhesive extracellular matrix proteins such as fibronectin and vitronectin, MAPK inhibitors, such as, for example, compounds disclosed in U.S. Published Application 2004/0209901 and U.S. Published Application 2004/0132729.

The incorporation of the cells of the present invention into a scaffold can be achieved by the simple depositing of cells onto the scaffold. Cells can enter into the scaffold by simple diffusion (J. Pediatr. Surg. 23 (1 Pt 2): 3-9 (1988)). Several other approaches have been developed to enhance the efficiency of cell seeding. For example, spinner flasks have been used in seeding of chondrocytes onto polyglycolic acid scaffolds (Biotechnol. Prog. 14(2): 193-202 (1998)). Another approach for seeding cells is the use of centrifugation, which yields minimum stress to the seeded cells and enhances seeding efficiency. For example, Yang et al. developed a cell seeding method (J. Biomed. Mater. Res. 55(3): 379-86 (2001)), referred to as Centrifugational Cell Immobilization (CCI).

The present invention is further illustrated, but not limited by, the following examples.

EXAMPLES

For clarity of disclosure, and not by way of limitation, the detailed description of the invention is divided into the following subsections that describe or illustrate certain features, embodiments, or applications of the present invention.

Example 1 Human Embryonic Stem Cell Culture

The human embryonic stem cell lines H1, H7, and H9 were obtained from WiCell Research Institute, Inc., (Madison, Wis.) and cultured according to instructions provided by the source institute. The human embryonic stem cells were also seeded on plates coated with a 1:30 dilution of reduced growth factor MATRIGEL™ (BD Biosciences; Cat #356231) and cultured in MEF-conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB). The cells cultured on MATRIGEL™ were routinely passaged as clusters using collagenase IV (Invitrogen/GIBCO; Cat #17104-019), Dispase (Invitrogen; Cat #17105-041), or Liberase CI enzyme (Roche; Cat #11814435001). In some instances, the cells were passaged as single cells using ACCUTASE (Sigma; Cat #A6964).

Human embryonic stem cells used in these examples were maintained in an undifferentiated, pluripotent state with passage on average every four-days. Passage was performed by exposing cell cultures to a solution of collagenase (1 or 10 mg/ml; Sigma-Aldrich) for 10 to 30 minutes at 37° C. followed by gentle scraping with a pipette tip to recover cell clusters. Clusters were allowed to sediment by gravity, followed by washing to remove residual collagenase. Cell clusters were split at a 1:3 ratio for routine maintenance culture or a 1:1 ratio for later assay. All human ES cell lines were maintained at passage numbers less than 50 and routinely evaluated for normal karyotypic phenotype and absence of mycoplasma contamination.

Example 2 Bioassay for the Formation of Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage

Activin A is an important mediator of differentiation in a broad range of cell types, including differentiation of embryonic stem cells to definitive endoderm. When human embryonic stem cells are treated with a combination of activin A and Wnt3a, various genes representative of definitive endoderm are up-regulated. A bioassay that measures this differentiation in human embryonic stem cells was adapted in miniaturized format to 96-well plates for screening purposes. Validation was completed using treatment with commercial sources of activin A and Wnt3a recombinant proteins and measuring protein expression of the transcription factor SOX17, considered to be a representative marker of definitive endoderm.

Live Cell Assay:

Briefly, clusters of H1 human embryonic stem cells were grown on reduced growth factor MATRIGEL™ (Invitrogen; Cat #356231)-coated tissue culture plastic. Cells were passaged using collagenase (Invitrogen; Cat #17104-019) treatment and gentle scraping, washed to remove residual enzyme, and plated in a ratio of 1:1 (surface area) on reduced growth factor MATRIGEL™-coated 96-well black plates (Packard ViewPlates; Perkin Elmer; Cat #6005182). Cells were allowed to attach as clusters and then recover log phase growth over a 1 to 3 day period, feeding daily with 100 μl per well mouse embryonic fibroblast (MEF) conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB).

The assay was initiated by washing the wells of each plate twice in PBS (Invitrogen; Cat #14190), followed by adding an aliquot (100 μl) of test sample in DMEM:F12 basal medium (Invitrogen; Cat #11330-032) to each well. Test conditions were performed in triplicate, feeding on alternate days by aspirating and replacing the medium from each well with test samples over a total four-day assay period. On the first and second day of assay, test samples added to the assay wells were diluted in DMEM:F12 with 0.5% FCS (HyClone; Cat #SH30070.03) and 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN). On the third and fourth day of assay, test samples added to the assay wells were diluted in DMEM:F12 with 2% FCS, without any Wnt3a. Positive control samples consisted of recombinant human activin A (PeproTech; Cat #120-14) added at a concentration of 100 ng/ml throughout assay plus Wnt3a (20 ng/ml) on days 1 and 2. Negative control samples omitted treatment with both activin A and Wnt3a.

High Content Analysis:

At the conclusion of four-days of culture, assay plates were washed twice with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for one hour at room temperature. Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Molecular Probes; Cat #AZ1467) was diluted 1:200 in PBS and added to each sample well after washing three times with PBS. To counter stain nuclei, 4 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for ten minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Exposure times were optimized from positive control wells and from untreated negative control wells stained with secondary antibody alone. Images from 15 fields per well were acquired to compensate for any cell loss during the bioassay and subsequent staining procedures. Measurements for total cell number and total SOX17 intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria of gray-scale ranges between 200 to 3500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control. Normalized data were calculated for averages and standard deviations for each replicate set.

FIG. 1 shows validation of the screening assay, testing a two-fold dilution curve of a commercial source of activin A (PeproTech) and measuring both cell number (FIG. 1A) and SOX17 intensity (FIG. 1B). Optimal activin A effects for induction of SOX17 expression were generally observed in the 100-200 ng/ml range with an EC₅₀ of 30-50 ng/ml. Omitting Wnt3a from treatment on days 1 and 2 of assay failed to produce measurable SOX17 expression (FIG. 1B, white bars). Absence of activin A also failed to yield SOX17 expression (FIG. 1B).

Example 3 Primary Screening: Effects of the Compounds of the Present Invention on the Differentiation of Human Embryonic Stem Cells into Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage in the Absence of Activin A

Differentiation of pluripotent stem cells into cells expressing markers characteristic of the definitive endoderm lineage is mediated through a series of receptor-ligand interactions that in turn activate receptor kinases leading to phosphorylation and nuclear translocation of downstream substrates, eventually regulating expression of specific target genes. Optimal activation of these signaling cascades in some cell types may require inhibition of opposing default pathways. In other cases, redundant pathways involving alternative members of a larger kinase family may substitute in part for one or more signaling molecules. In other cases, canonical and non-canonical pathways may diverge with different initiating stimuli but may lead to a similar functional outcome.

Cell-based functional screens are one approach to identify novel targets and methods that can impact specific cellular responses. One very powerful approach involves a series of iterative screens whereby leads or hits from one screen are integrated into a subsequent screen. Alternatively, a series of different variables are integrated in a combinatorial fashion (for example, growth factors with kinase inhibitors) to identify novel effects on cellular differentiation. In this case, a library of small molecules comprising aniline-pyridinotriazines, cyclic aniline-pyridinotriazines and intermediate structures in their synthesis was tested for properties important during definitive endoderm differentiation of human embryonic stem cells, specifically for effects to retain or enhance cell number at the conclusion of a ‘first’ differentiation step in low serum and in the absence of the growth factor activin A.

Screening Assay

Cell Assay Seeding:

Briefly, clusters of H1 human embryonic stem cells were grown on reduced growth factor MATRIGEL™ (Invitrogen; Cat #356231)-coated tissue culture plastic. Cells were passaged using collagenase (Invitrogen; Cat #17104-019) treatment and gentle scraping, washed to remove residual enzyme, and plated with even dispersal at a ratio of 1:1 (surface area) on reduced growth factor MATRIGEL™-coated 96-well black plates (Packard ViewPlates; PerkinElmer; Cat #6005182) using volumes of 100 μl/well. Cells were allowed to attach as clusters and then recover log phase growth over a 1 to 3 day period, feeding daily with MEF conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB). Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of assay.

Preparation of Compounds and Assay:

The compounds tested were made available as 5 mM stocks in 96-well plate format, solubilized in 100% DMSO (Sigma; Cat #D2650) and stored at −80° C. The library compounds were further diluted to an intermediate concentration of 0.2 mM in 50 mM HEPES (Invitrogen; Cat #15630-080), 20% DMSO and stored at 4° C. Test conditions were performed in triplicate, feeding on alternate days over a four-day assay period. Primary screening assays were initiated by aspirating culture medium from each well followed by three washes in PBS (Invitrogen; Cat #14190) to remove residual growth factors and serum. On the first day of assay, test volumes of 200 μl per well were added back containing DMEM:F12 base medium (Invitrogen; Cat #11330-032) supplemented with 0.5% FCS (HyClone; Cat #SH30070.03) and 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN) plus 2.5 μM test compound. On the third day of assay, test volumes of 200 μl per well were added back containing DMEM:F12 base medium supplemented with 2% FCS plus 2.5 μM test compound, without Wnt3a. Positive control samples contained the same base medium supplemented with FCS, substituting 100 ng/ml recombinant human activin A (PeproTech; Cat #120-14) for the test compound throughout the four-day assay along with Wnt3a (20 ng/ml) added only on days 1 and 2. Negative control samples contained DMEM:F12 base medium supplemented with FCS, adding Wnt3a on days 1 and 2 but omitting activin A.

High Content Analysis:

At the conclusion of four-days of culture, assay plates were washed twice with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for one hour at room temperature. Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Molecular Probes; Cat #AZ1467) was diluted 1:200 in PBS and added to each sample well after washing three times with PBS. To counter stain nuclei, 4 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for ten minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Exposure times were optimized from positive control wells and from untreated negative control wells stained with secondary antibody alone. Images from 15 fields per well were acquired to compensate for any cell loss during the bioassay and subsequent staining procedures. Measurements for total cell number and total SOX17 intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria of gray-scale ranges between 200 to 3500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control. Normalized data were calculated for averages and standard deviations for each replicate set.

Table 1 shows results of primary screening for the compounds tested, showing their effects on the differentiation of human embryonic stem cells to cells expressing markers characteristic of the definitive endoderm lineage in the absence of activin A. The results include quantitative measures of both cell number and SOX17 intensity, where respective data points were averaged from triplicate wells and analyzed for each parameter using identical fields in each well. Expression of the transcription factor SOX17 is considered indicative of definitive endoderm differentiation. Primary screening results were captured from eight 96-well screening plates. Plate to plate variability was reduced with inclusion of individual positive and negative controls on each plate. Results are normalized and expressed as a percentage of the positive control. Emphasis was placed on retention or amplification of cell number at the conclusion of assay.

Table 2 lists a subset of 27 compounds and their analyzed results from the primary screening, where these hits appeared to retain cell number at a level equivalent to or better than the positive control despite the absence of activin A in the screening assay.

In some cases, SOX17 expression was induced in the absence of activin A (for example, the cyclic aniline-pyridinotriazines Compound 35 and Compound 22.

The compounds shown in Table 2 were selected for further evaluation for effects on the differentiation of human embryonic stem cells to cells expressing markers characteristic of the definitive endoderm lineage in the absence of activin A.

Example 4 Secondary Screening: Effects of the Compounds of the Present Invention on the Differentiation of Human Embryonic Stem Cells into Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage with EGF/FGF4 in the Absence of Activin A

A titration curve for activin A with a constant amount of Wnt3a showed at least two effects during DE differentiation: 1) maintaining cell numbers or preventing cell loss; and 2) inducing a marker of DE, for example, SOX17 expression (Example 2). Primary screening from Example 3 identified compounds that could maintain similar or improved cell numbers in assay relative to addition of activin A/Wnt3a alone. A secondary screening assay was conducted to evaluate the effect of combinations of the identified compounds with other growth factors, specifically EGF and FGF4, on the generation of definitive endoderm.

Cell Assay Seeding:

Clusters of H1 human embryonic stem cells were grown on reduced growth factor MATRIGEL™ (Invitrogen; Cat #356231)-coated tissue culture plastic. Cells were passaged using collagenase (Invitrogen; Cat #Cat #17104-019) treatment and gentle scraping, washed to remove residual enzyme, and plated with even dispersal at a ratio of 1:1 (surface area) on reduced growth factor MATRIGEL™-coated 96-well black plates (Packard ViewPlates; PerkinElmer; Cat #6005182) using volumes of 100 μl/well. Cells were allowed to attach as clusters and then recover log phase growth over a 1 to 3 day period, feeding daily with MEF conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB). Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of assay.

Preparation of Compounds and Growth Factors:

Stock concentrations for EGF (R&D Systems; Cat #236-EG) and FGF4 (R&D Systems; Cat #235-F4) were 250 ng/ml, each solubilized in PBS with 0.1% BSA (Sigma; Cat #A7888). Compounds were available as 5 mM stocks in 96-well plate format, solubilized in 100% DMSO (Sigma; Cat #D2650) and stored at −80° C. The compounds were further diluted to an intermediate concentration of 0.2 mM in 50 mM HEPES (Invitrogen; Cat #15630-080), 20% DMSO and stored at 4° C. All growth factors and inhibitors were prepared in a deep well, 96-well polypropylene plate, diluted to 5× intermediate stocks in DMEM:F12 base medium at the beginning of assay and stored at 4° C.

A secondary screening assay was conducted, testing in triplicate and feeding on alternate days over the four-day assay timeframe. Assays were initiated by aspirating culture medium from each well followed by three washes in PBS to remove residual growth factors and serum. Test volumes of 80 μl per well were added back containing DMEM:F12 base medium (Invitrogen; Cat #11330-032) supplemented with 0.625% FCS (HyClone; Cat #SH30070.03), 25 ng/ml Wnt3a (R&D Systems), and 3.125 μM compound plus 20 μl 5× stock of growth factors to yield a final concentration of 0.5% FCS, 20 ng/ml Wnt3a, and 2.5 μM compound plus 50 ng/ml EGF and 50 ng/ml FGF4 in the assay. Positive control wells (100 μl/well) contained the same base medium supplemented with 0.5% FCS, 20 ng/ml Wnt3a and 100 ng/ml activin A. Negative control wells (100 μl/well) contained the same base medium with 0.5% FCS and 20 ng/ml Wnt3a, omitting activin A.

On day 3, wells were aspirated and fed with 80 μl DMEM:F12 base medium supplemented with 2.5% FCS (HyClone) and 3.125 μM compound plus 20 μl 5× stock of growth factors per well to yield a final concentration of 2% FCS and 2.5 μM compound (omitting Wnt3a) plus 50 ng/ml EGF and FGF4 in the assay. Positive control wells (100 μl/well) contained the same base medium supplemented with 2% FCS and 100 ng/ml activin A, omitting Wnt3a. Negative control wells (100 μl/well) contained the same base medium with 2% FCS, omitting both activin A and Wnt3a.

High Content Analysis:

At the conclusion of four-days of culture, assay plates were washed twice with PBS, fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for one hour at room temperature. Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Molecular Probes; Cat #AZ1467) was diluted 1:200 in PBS and added to each sample well after washing three times with PBS. To counterstain nuclei, 4 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for ten minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Exposure times were optimized from positive control wells and from untreated negative control wells stained with secondary antibody alone. Images from 15 fields per well were acquired to compensate for any cell loss during the bioassay and subsequent staining procedures. Measurements for total cell number and total SOX17 intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria of gray-scale ranges between 200 to 3500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control. Normalized data were calculated for averages and standard deviations for each replicate set.

Table 3A shows the results for two growth factors, EGF and FGF 4 (50 ng/ml each) tested in combination with the aniline-pyridinotriazine compounds shown in Table 2 for their effects on the differentiation of human embryonic stem cells into cells expressing markers characteristic of the definitive endoderm lineage in the absence of activin A. Results are ranked in descending order for best effects on SOX17 expression. Although the effects of these compounds on SOX17 expression were considered weak relative to the activin A/Wnt3a positive control, the responses for some of these compounds were considered significant. For example a selection of the compounds appear to have unique properties with respect to retaining high cell numbers per well during assay, presumably either by preventing apoptosis or by modulating cell cycle. In addition, these compounds appear to synergize with EGF and FGF4 to promote modest definitive endoderm differentiation, as measured by SOX17 expression. The most potent compounds are listed in Table 3B. Other compounds tested in combination with EGF and FGF4 in this assay were ineffective at inducing SOX17 expression but could retain cell numbers in assay (e.g. Compound 90: 85% cell number; 2% SOX17 expression).

Example 5 Effects of Compounds of the Present Invention in Combination with Other Factors on the Differentiation of Human Embryonic Stem Cells to Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage in the Absence of Activin A

A secondary assay was conducted to evaluate the effect of the compounds of the present invention with combinations of other individual growth factors or compounds known from the literature to regulate definitive endoderm differentiation.

Cell Assay Seeding:

Clusters of H1 human embryonic stem cells were grown on reduced growth factor MATRIGEL™ (Invitrogen; Cat #356231)-coated tissue culture plastic. Cells were passaged using collagenase (Invitrogen; Cat #Cat #17104-019) treatment and gentle scraping, washed to remove residual enzyme, and plated with even dispersal at a ratio of 1:1 (surface area) on reduced growth factor MATRIGEL™-coated 96-well black plates (Packard ViewPlates; PerkinElmer; Cat #6005182) using volumes of 100 μl/well. Cells were allowed to attach as clusters and then recover log phase growth over a 1 to 3 day period, feeding daily with MEF conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB). Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of assay.

Preparation of Compounds and Growth Factors:

Stocks of growth factors purchased from R&D Systems were EGF (Cat #236-EG), FGF4 (Cat #235-F4), PDGF-A (Cat #221-AA), PDGF-B (Cat #220-BB), PDGF-C(Cat #1687-CC), PDGF-D (Cat #1159-SB), PDGF-A/B (Cat #222-AB), VEGF (Cat #293-VE), BMP-1 (Cat #1927-ZN) BMP-2 (Cat #355-BM), BMP-4 (Cat #314-BP), BMP-6 (Cat #507-BP), BMP-7 (Cat #222-AB), BMP-2/7 (Cat #3229-BM). Other agents tested were purchased as follows: BMP-7 (Sigma; Cat #B1434), LY294002 (Cayman; Cat 70920), PD98059, U0126, U0124 (EMD Biosciences; Cat #453710), muscimol (Tocris; Cat #0289), biuculline (Tocris; Cat #0130), sodium butyrate (Sigma; Cat #B5887). All growth factors were solubilized in PBS with 0.1% BSA (Sigma; Cat #A7888) and stored frozen at −80° C. Small molecules were solubilized in 100% DMSO (Sigma; Cat #D2650) and stored frozen at −80° C. The compounds were available as 5 mM stocks in 96-well plate format, solubilized in 100% DMSO and stored at −80° C. The compounds of the present invention were further diluted to an intermediate concentration of 0.2 mM in 50 mM HEPES (Invitrogen; Cat #15630-080), 20% DMSO and stored at 4° C. All growth factors and inhibitors were prepared in a deep well, 96-well polypropylene plate, diluted to 5× intermediate stocks in DMEM:F12 base medium at the beginning of assay and stored at 4° C.

A secondary screening assay was conducted, testing in triplicate and feeding on alternate days over the four-day assay timeframe. Assays were initiated by aspirating culture medium from each well followed by three washes in PBS to remove residual growth factors and serum. Test volumes of 80 μl per well were added back containing DMEM:F12 base medium (Invitrogen; Cat #11330-032) supplemented with 0.625% FCS (HyClone; Cat #SH30070.03), 25 ng/ml Wnt3a (R&D Systems), and 3.125 μM compound plus 20 μl 5× stock of growth factor or small molecule to yield a final concentration of 0.5% FCS, 20 ng/ml Wnt3a, and 2.5 μM compound. All remaining growth factors were tested at a final assay concentration of 50 ng/ml (EGF, FGF4, PDGF-A, PDGF-B, PDGF-C, PDGF-D, PDGF-A/B, VEGF, BMP-1, BMP-2, BMP-4, BMP-6, BMP-7, BMP-2/7). Final assay concentrations of small molecules tested were as follows: muscimol (20 μM), PD98059 (1 μM), LY294002 (2.5 μM), U0124 (1 μM), U0126 (1 μM), sodium butyrate (0.5 mM). Positive control wells (100 μl/well) contained the same base medium supplemented with 0.5% FCS, 20 ng/ml Wnt3a and 100 ng/ml activin A. Negative control wells (100 μl/well) contained the same base medium with 0.5% FCS and 20 ng/ml Wnt3a, omitting activin A.

On day 3, wells were aspirated and fed with 80 μl DMEM:F12 base medium supplemented with 2.5% FCS (HyClone) and 3.125 μM cyclic aniline-pyridinotriazine compound plus 20 μl 5× stock of growth factors or small molecules per well to yield a final concentration of 2% FCS and 2.5 μM compound (omitting Wnt3a) and as denoted on day one for all remaining growth factors or small molecules. Positive control wells (100 μl/well) contained the same base medium supplemented with 2% FCS and 100 ng/ml activin A, omitting Wnt3a. Negative control wells (100 μl/well) contained the same base medium with 2% FCS, omitting both activin A and Wnt3a.

High Content Analysis:

At the conclusion of four-days of culture, assay plates were washed twice with PBS, fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for one hour at room temperature. Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Molecular Probes; Cat #AZ1467) was diluted 1:200 in PBS and added to each sample well after washing three times with PBS. To counterstain nuclei, 4 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for ten minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Exposure times were optimized from positive control wells and from untreated negative control wells stained with secondary antibody alone. Images from 15 fields per well were acquired to compensate for any cell loss during the bioassay and subsequent staining procedures. Measurements for total cell number and total SOX17 intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria of gray-scale ranges between 200 to 3500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control. Normalized data were calculated for averages and standard deviations for each replicate set.

Table 4 shows the results for the differentiation of human embryonic stem cells into cells expressing markers characteristic of the definitive endoderm lineage following treatment with the compounds of the present invention in combination with individual growth factors or other small molecules. In general, members of the BMP family (BMP-1, BMP-2, BMP-4, BMP-6, BMP-7, BMP-2/7) inhibited or had negligible effects on SOX17 expression. The same was true for most of the small molecule enzyme inhibitors tested in this assay (LY294002, PD98059, U0126, U0124, sodium butyrate). However, some members of the PDGF family (PDGF-A, -AB, -C, and -D) provided an increase in SOX17 expression (10-25% of the activin A/Wnt3a control). Other growth factors showing similar increases in SOX17 expression included EGF (34%), VEGF (18%), and FGF4 (17%), although FGF4 was not able to support retention of cell numbers. The small molecule muscimol (GABA_(A) receptor agonist) tested in combination with Compound 35 also provided a modest increase in SOX17 expression; the GABA_(A) antagonist bicuculline had no effect on SOX17 expression. EGF, FGF4, PDGF-A, PDGF-B, PDGF-AB, PDGF-C, and PDGF-D and muscimol were selected for additional evaluation during definitive endoderm differentiation.

Example 6 Effects of the Compounds of the Present Invention in Combination with Other Factors on the Differentiation of Human Embryonic Stem Cells into Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage in the Absence of Activin A

A secondary assay was conducted to evaluate the effects of combinations of different compounds with other individual agents on definitive endoderm differentiation. The other agents selected for this screen had previously shown a modest increase in definitive endoderm formation, as tested with Compound 17 and as denoted in Table 5. In this screen, a broader panel of compounds was evaluated in with these agents, either in single pair-wise comparisons or pooled combinations.

Cell Assay Seeding:

Clusters of H1 human embryonic stem cells were grown on reduced growth factor MATRIGEL™ (Invitrogen; Cat #356231)-coated tissue culture plastic. Cells were passaged using collagenase (Invitrogen; Cat #17104-019) treatment and gentle scraping, washed to remove residual enzyme, and plated with even dispersal at a ratio of 1:1 (surface area) on reduced growth factor MATRIGEL™-coated 96-well black plates (Packard ViewPlates; PerkinElmer; Cat #6005182) using volumes of 100 μl/well. Cells were allowed to attach as clusters and then recover log phase growth over a 1 to 3 day period, feeding daily with MEF-conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB). Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of the assay.

Preparation of Compounds and Growth Factors:

Stocks of growth factors purchased from R&D Systems were EGF (Cat #236-EG), FGF4 (Cat #235-F4), PDGF-A (Cat #221-AA), PDGF-D (Cat #1159-SB), PDGF-A/B (Cat #222-AB), and VEGF (Cat #293-VE). Muscimol was purchased from Tocris (Cat #0289). All growth factors were solubilized in PBS with 0.1% BSA (Sigma; Cat #A7888) and stored frozen at −80° C. Muscimol was solubilized in 100% DMSO (Sigma; Cat #D2650) and stored frozen at −80° C. Compounds were available as 5 mM stocks in 96-well plate format, solubilized in 100% DMSO and stored at −80° C. Compounds were further diluted to an intermediate concentration of 0.2 mM in 50 mM HEPES (Invitrogen; Cat #15630-080), 20% DMSO and stored at 4° C. All growth factors and inhibitors were prepared in a deep well, 96-well polypropylene plate, diluted to 5× intermediate stocks in DMEM:F12 base medium at the beginning of assay and stored at 4° C.

A secondary screening assay was conducted, testing in triplicate and feeding on alternate days over the four-day assay timeframe. Assays were initiated by aspirating culture medium from each well followed by three washes in PBS to remove residual growth factors and serum. Test volumes of 80 μl per well were added back containing DMEM:F12 base medium (Invitrogen; Cat #11330-032) supplemented with 0.625% FCS (HyClone; Cat #SH30070.03), 25 ng/ml Wnt3a (R&D Systems), and 3.125 μM compound plus 20 μl 5× stock of growth factor or small molecule to yield a final concentration of 0.5% FCS, 20 ng/ml Wnt3a, and 2.5 μM. All remaining growth factors were tested at a final assay concentration of 50 ng/ml (EGF, FGF4, PDGF-A, PDGF-A/B, VEGF). Final assay concentration of muscimol was 20 μM. Positive control wells (100 μl/well) contained the same base medium supplemented with 0.5% FCS, 20 ng/ml Wnt3a and 100 ng/ml activin A. Negative control wells (100 μl/well) contained the same base medium with 0.5% FCS and 20 ng/ml Wnt3a, omitting activin A.

On day 3, wells were aspirated and fed with 80 μl DMEM:F12 base medium supplemented with 2.5% FCS (HyClone) and 3.125 μM compound plus 20 μl 5× stock of growth factors or small molecules per well to yield a final concentration of 2% FCS and 2.5 μM compound (omitting Wnt3a) and as denoted on day one for all remaining growth factors or small molecules. Positive control wells (100 μl/well) contained the same base medium supplemented with 2% FCS and 100 ng/ml activin A, omitting Wnt3a. Negative control wells (100 μl/well) contained the same base medium with 2% FCS, omitting both activin A and Wnt3a.

High Content Analysis:

At the conclusion of four-days of culture, assay plates were washed twice with PBS, fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for one hour at room temperature. Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Molecular Probes; Cat #AZ1467) was diluted 1:200 in PBS and added to each sample well after washing three times with PBS. To counterstain nuclei, 4 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for ten minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Exposure times were optimized from positive control wells and from untreated negative control wells stained with secondary antibody alone. Images from 15 fields per well were acquired to compensate for any cell loss during the bioassay and subsequent staining procedures. Measurements for total cell number and total SOX17 intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on grayscale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria of gray-scale ranges between 200 to 3500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control. Normalized data were calculated for averages and standard deviations for each replicate set.

Table 5 shows compounds previously identified as hits (Table 2) tested in a definitive endoderm bioassay in various combinations with growth factors and muscimol, without activin A. Some compounds had minimal or weak effects on SOX17 expression with all growth factor combinations tested. However, some compounds were able to induce significant SOX17 expression with some but not all growth factor combinations. One compound in particular, Compound 34, had significant synergistic responses with all growth factors tested and mediated increases in both cell numbers as well as SOX17 expression in this assay: Compound 39 with 1) EGF+FGF4=77% of positive control response; or 2) EGF+FGF4+PDGF-AB=68% of positive control response; or 3) EGF+FGF4+PDGF-A+VEGF=31% of positive control response.

Example 7 Effects of Compound 34 in Combination with Other Factors on the Differentiation of Human Embryonic Stem Cells into Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage in the Absence of Activin A

In this example, an effort was made to analyze the minimum number of growth factors required in combination with the best cyclic aniline-pyridinotriazine compound, Compound 34 to yield a robust SOX17 response in the absence of activin A. Also in this example, a new growth factor, GDF-8, was added for evaluation. GDF-8, also known as myostatin, is a member of the TGF-β family and has been shown to use the activin type II and TGF-β type I receptors (ALK4/5) to induce SMAD 2/3 phosphorylation.

Cell Assay Seeding:

Clusters of H1 human embryonic stem cells were grown on reduced growth factor MATRIGEL™ (Invitrogen; Cat #356231)-coated tissue culture plastic. Cells were passaged using collagenase (Invitrogen; Cat #17104-019) treatment and gentle scraping, washed to remove residual enzyme, and plated with even dispersal at a ratio of 1:1 (surface area) on reduced growth factor MATRIGEL™-coated 96-well black plates (Packard ViewPlates; PerkinElmer; Cat #6005182) using volumes of 100 μl/well. Cells were allowed to attach as clusters and then recover log phase growth over a 1 to 3 day period, feeding daily with MEF conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB). Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of assay.

Preparation of Compounds and Growth Factors:

Stocks of growth factors purchased from R&D Systems were EGF (Cat #236-EG), FGF4 (Cat #235-F4), PDGF-A (Cat #221-AA), PDGF-D (Cat #1159-SB), PDGF-A/B (Cat #222-AB), VEGF (Cat #293-VE), and GDF-8 (Cat #788-G8). Muscimol was purchased from Tocris (Cat #0289). All growth factors were solubilized in PBS with 0.1% BSA (Sigma; Cat #A7888) and stored frozen at −80° C. Muscimol was solubilized in 100% DMSO (Sigma; Cat #D2650) and stored frozen at −80° C. Cyclic aniline-pyridinotriazine compounds were available as 5 mM stocks in 96-well plate format, solubilized in 100% DMSO and stored at −80° C. Compound 34 was further diluted to an intermediate concentration of 0.2 mM in 50 mM HEPES (Invitrogen; Cat #15630-080), 20% DMSO and stored at 4° C. All growth factors and inhibitors were prepared in a deep well, 96-well polypropylene plate, diluted to 5× intermediate stocks in DMEM:F12 base medium at the beginning of assay and stored at 4° C.

A secondary screening assay was conducted, testing in triplicate and feeding on alternate days over the four-day assay timeframe. Assays were initiated by aspirating culture medium from each well followed by three washes in PBS to remove residual growth factors and serum. Test volumes of 80 μl per well were added back containing DMEM:F12 base medium (Invitrogen; Cat #11330-032) supplemented with 0.625% FCS (HyClone; Cat #SH30070.03), 25 ng/ml Wnt3a (R&D Systems), and 3.125 μM Compound 27 plus 20 μl 5× stock of growth factor or small molecule to yield a final concentration of 0.5% FCS, 20 ng/ml Wnt3a, and 2.5 μM Compound 34. All remaining growth factors were tested at a final assay concentration of 50 ng/ml (EGF, FGF4, PDGF-A, PDGF-A/B, VEGF) with the exception of GDF-8 tested at 25 ng/ml. Final assay concentration of muscimol was 20 μM. Positive control wells (100 μl/well) contained the same base medium supplemented with 0.5% FCS, 20 ng/ml Wnt3a and 100 ng/ml activin A. Negative control wells (100 μl/well) contained the same base medium with 0.5% FCS and 20 ng/ml Wnt3a, omitting activin A.

On day 3, wells were aspirated and fed with 80 μl DMEM:F12 base medium supplemented with 2.5% FCS (HyClone) and 3.125 μM Compound 34 plus 20 μl 5× stock of growth factors or small molecules per well to yield a final concentration of 2% FCS and 2.5 μM Compound 34 (omitting Wnt3a) and as denoted on day one for all remaining growth factors or small molecules. Positive control wells (100 μl/well) contained the same base medium supplemented with 2% FCS and 100 ng/ml activin A, omitting Wnt3a. Negative control wells (100 μl/well) contained the same base medium with 2% FCS, omitting both activin A and Wnt3a.

High Content Analysis:

At the conclusion of four-days of culture, assay plates were washed twice with PBS, fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for one hour at room temperature. Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Molecular Probes; Cat #AZ1467) was diluted 1:200 in PBS and added to each sample well after washing three times with PBS. To counterstain nuclei, 4 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for ten minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Exposure times were optimized from positive control wells and from untreated negative control wells stained with secondary antibody alone. Images from 15 fields per well were acquired to compensate for any cell loss during the bioassay and subsequent staining procedures. Measurements for total cell number and total SOX17 intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria of gray-scale ranges between 200 to 3500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control. Normalized data were calculated for averages and standard deviations for each replicate set.

Table 6 shows results of this assay. Where GDF-8 was present in any combination with the Compound 34, a substantial increase in SOX17 expression was observed. Furthermore, GDF-8 and Wnt3a with Compound 34 were sufficient to yield SOX17 expression (88% of control) in a range similar to that seen with 100 ng/ml activin A/Wnt3a treatment. It appears that the growth factor GDF-8 can serve as a replacement for activin A during definitive endoderm differentiation of human embryonic stem cells.

Example 8 Additional Screening for Compounds Capable of Differentiating Pluripotent Stem Cells into Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage

Based on the compound structures for hits identified thus far, an analog search was conducted to find additional related compounds to test in the definitive endoderm bioassay. The substructure search yielded compounds for screening. Screening parameters for this assay were designed with the combination of factors that had yielded optimal results in previous assays, specifically combining EGF, FGF, PDGF-A, VEGF, PDGF-D, muscimol, and GDF-8 with the small molecule compound.

Cell Assay Seeding:

Briefly, clusters of H1 human embryonic stem cells were grown on reduced growth factor MATRIGEL™ (Invitrogen; Cat #356231)-coated tissue culture plastic. Cells were passaged using collagenase (Invitrogen; Cat #17104-019) treatment and gentle scraping, washed to remove residual enzyme, and plated with even dispersal at a ratio of 1:1 (surface area) on reduced growth factor MATRIGEL™-coated 96-well black plates (Packard ViewPlates; PerkinElmer; Cat #6005182) using volumes of 100 μl/well. Cells were allowed to attach as clusters and then recover log phase growth over a 1 to 3 day period, feeding daily with MEF conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB). Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of assay.

Preparation of Compounds and Assay:

Growth factors purchased from R&D Systems were EGF (Cat #236-EG), FGF4 (Cat #235-F4), PDGF-A (Cat #221-AA), PDGF-D (Cat #1159-SB), PDGF-A/B (Cat #222-AB), VEGF (Cat #293-VE), and GDF-8 (Cat #788-G8). Muscimol was purchased from Tocris (Cat #0289). Screening was conducted using a library of compounds that were made available as 5 mM stocks in 96-well plate format, solubilized in 100% DMSO (Sigma; Cat #D2650) and stored at −80° C. The compounds were further diluted to an intermediate concentration of 0.2 mM in 50 mM HEPES (Invitrogen; Cat #15630-080), 20% DMSO and stored at 4° C. Test conditions were performed in single wells, feeding on alternate days over a four-day assay period. Primary screening assays were initiated by aspirating culture medium from each well followed by three washes in PBS (Invitrogen; Cat #14190) to remove residual growth factors and serum. On the first day of assay, test volumes of 200 μl per well were added back containing DMEM:F12 base medium (Invitrogen; Cat #11330-032) supplemented with 0.5% FCS (HyClone; Cat #SH30070.03) and 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN) plus 2.5 μM compound. All remaining growth factors were tested at a final assay concentration of 50 ng/ml (EGF, FGF4, PDGF-A, PDGF-A/B, VEGF) with the exception of GDF-8 tested at 25 ng/ml. Final assay concentration of muscimol was 20 μM. Positive control samples contained the same base medium supplemented with 0.5% FCS plus 20 ng/ml Wnt3a and 100 ng/ml recombinant human activin A (PeproTech; Cat #120-14). Negative control samples contained DMEM:F12 base medium supplemented with 0.5% FCS and 20 ng/ml Wnt3a. On the third day of assay, test volumes of 200 μl per well were added back containing DMEM:F12 base medium supplemented with 2% FCS plus 2.5 μM compound, without Wnt3a. All remaining growth factors were tested at a final assay concentration of 50 ng/ml (EGF, FGF4, PDGF-A, PDGF-A/B, VEGF) with the exception of GDF-8 tested at 25 ng/ml. Final assay concentration of muscimol was 20 μM. Positive control samples contained the same base medium supplemented with 2% FCS and 100 ng/ml recombinant human activin A (PeproTech; Cat #120-14). Negative control samples contained DMEM:F12 base medium supplemented with 2% FCS. Positive control samples contained the same base medium supplemented with FCS, substituting 100 ng/ml recombinant human activin A (PeproTech; Cat #120-14) for the aniline-pyridinotriazine compound throughout the four-day assay along with Wnt3a (20 ng/ml) on days 1 and 2. Negative control samples contained DMEM:F12 base medium supplemented with FCS, adding Wnt3a on days 1 and 2 but omitting treatment with activin A.

High Content Analysis:

At the conclusion of four-days of culture, assay plates were washed twice with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for one hour at room temperature. Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Molecular Probes; Cat #AZ1467) was diluted 1:200 in PBS and added to each sample well after washing three times with PBS. To counterstain nuclei, 4 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for ten minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Exposure times were optimized from positive control wells and from untreated negative control wells stained with secondary antibody alone. Images from 15 fields per well were acquired to compensate for any cell loss during the bioassay and subsequent staining procedures. Measurements for total cell number and total SOX17 intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell times area of the cell. Background was eliminated based on acceptance criteria of gray-scale ranges between 200 to 3500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control. Normalized data were calculated for averages and standard deviations for each replicate set.

In Table 7, GDF-8 and a combination of growth factors/agonists (EGF, FGF, PDGF-A, VEGF, PDGF-D, muscimol) were tested with a new set of aniline-pyridinotriazine compounds. Results from two assay plates in this single experiment are ranked with respect to SOX17 responses (as a percentage of the positive control treatment with activin A and Wnt3a). Additional compounds were identified that show significant synergistic activity with the growth factor/agonist pool. These compounds were effective in both retaining assay cell number and yielding SOX17 expression during human embryonic stem cell differentiation in the absence of activin A. A list of these hits with greater than 25% activity of the positive control is shown in Table 8.

Of note, four hits from the initial primary screening (Table 2) were duplicated in the analog library. Two of these compounds repeated as hits with the analog screening (Compound 34 and Compound 35; shown boxed in Table 8); one was a weak hit in the analog screening, and one compound did not repeat.

Example 9 Effects of the Compounds of the Present Invention on the Differentiation of Human Embryonic Stem Cells to Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage in the Presence of Low Concentrations of Activin A

It was important to determine if the compounds that had been identified as hits in the definitive endoderm bioassays above could also show synergistic activity with very low doses of activin A. An initial evaluation was performed using the short hit list of cyclic aniline-pyridinotriazine compounds denoted in Table 3B.

Cell Assay Seeding:

Clusters of H1 human embryonic stem cells were grown on reduced growth factor MATRIGEL™ (Invitrogen; Cat #356231)-coated tissue culture plastic. Cells were passaged using collagenase (Invitrogen; Cat #17104-019) treatment and gentle scraping, washed to remove residual enzyme, and plated with even dispersal at a ratio of 1:1 (surface area) on reduced growth factor MATRIGEL™-coated 96-well black plates (Packard ViewPlates; PerkinElmer; Cat #6005182) using volumes of 100 μl/well. Cells were allowed to attach as clusters and then recover log phase growth over a 1 to 3 day period, feeding daily with MEF conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB). Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of assay.

Preparation of Compounds and Growth Factors:

Stocks of growth factors purchased from R&D Systems were EGF (Cat #236-EG), FGF4 (Cat #235-F4), PDGF-A (Cat #221-AA), PDGF-D (Cat #1159-SB), PDGF-A/B (Cat #222-AB), VEGF (Cat #293-VE), and GDF-8 (Cat #788-G8). Activin A was purchased from PeproTech (Cat #). Muscimol was purchased from Tocris (Cat #0289). All growth factors were solubilized in PBS with 0.1% BSA (Sigma; Cat #A7888) and stored frozen at −80° C. Muscimol was solubilized in 100% DMSO (Sigma; Cat #D2650) and stored frozen at −80° C. The compounds were available as 5 mM stocks in 96-well plate format, solubilized in 100% DMSO and stored at −80° C. The compounds were further diluted to an intermediate concentration of 0.2 mM in 50 mM HEPES (Invitrogen; Cat #15630-080), 20% DMSO and stored at 4° C. All growth factors and inhibitors were prepared in a deep well, 96-well polypropylene plate, diluted to 5× intermediate stocks in DMEM:F12 base medium at the beginning of assay and stored at 4° C.

A secondary screening assay was conducted, testing in triplicate and feeding on alternate days over the four-day assay timeframe. Assays were initiated by aspirating culture medium from each well followed by three washes in PBS to remove residual growth factors and serum. Test volumes of 80 μl per well were added back containing DMEM:F12 base medium (Invitrogen; Cat #11330-032) supplemented with 0.625% FCS (HyClone; Cat #SH30070.03), 25 ng/ml Wnt3a (R&D Systems), 12.5 ng/ml activin A, and 3.125 μM compound plus 20 μl 5× stock of growth factor or small molecule to yield a final concentration of 0.5% FCS, 20 ng/ml Wnt3a, 10 ng/ml activin A, and 2.5 μM compound. All remaining growth factors were tested at a final assay concentration of 50 ng/ml (EGF, FGF4, PDGF-A, PDGF-A/B, VEGF), with the exception of GDF-8 used at 25 ng/ml. Final assay concentration of muscimol was 20 μM. Positive control wells (100 μl/well) contained the same base medium supplemented with 0.5% FCS, 20 ng/ml Wnt3a and 10 ng/ml (low dose) or 100 ng/ml (high dose) activin A. Negative control wells (100 μl/well) contained the same base medium with 0.5% FCS and 20 ng/ml Wnt3a, omitting activin A.

On day 3, wells were aspirated and fed with 80 μl DMEM:F12 base medium supplemented with 2.5% FCS (HyClone), 12.5 ng/ml activin A, and 3.125 μM compound plus 20 μl 5× stock of growth factors or small molecules per well to yield a final concentration of 2% FCS, 10 ng/ml activin A, and 2.5 μM compound (omitting Wnt3a) and as denoted on day one for all remaining growth factors or small molecules. Positive control wells (100 μl/well) contained the same base medium supplemented with 2% FCS and 10 ng/ml or 100 ng/ml activin A, omitting Wnt3a. Negative control wells (100 μl/well) contained the same base medium with 2% FCS, omitting both activin A and Wnt3a.

High Content Analysis:

At the conclusion of four-days of culture, assay plates were washed twice with PBS, fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for one hour at room temperature. Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Molecular Probes; Cat #AZ1467) was diluted 1:200 in PBS and added to each sample well after washing three times with PBS. To counterstain nuclei, 4 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for ten minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Exposure times were optimized from positive control wells and from untreated negative control wells stained with secondary antibody alone. Images from 15 fields per well were acquired to compensate for any cell loss during the bioassay and subsequent staining procedures. Measurements for total cell number and total SOX17 intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria of gray-scale ranges between 200 to 3500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control. Normalized data were calculated for averages and standard deviations for each replicate set.

Table 9 shows results from assay of various compounds and different combinations of growth factors with low doses of activin A. Some compounds showed robust synergistic responses with various growth factors. In other cases, the synergistic effects were more modest but significant relative to a low dose activin A control. Other compounds had no activity relative to the low dose activin A control.

Example 10 Effects of the Compounds of the Present Invention on the Differentiation of Single Human Embryonic Stem Cells to Cells Expressing Markers of the Definitive Endoderm Lineage in the Absence of Activin A

Cyclic aniline-pyridinotriazine compounds were also tested in a screening format using cells dispersed through enzymatic treatment to single cells and plated in monolayer for assay. The assay also made changes to eliminate serum that can provide growth factors even at low doses. To that end, the basal medium was changed and serum was replaced with fatty acid free BSA. The assay was shortened from four days to three days to provide a more narrow timeframe to measure results. Finally, the assay included two growth factors, EGF and FGF4 that had previously shown significant but sub-optimal effects on definitive endoderm differentiation in the absence of activin A.

Screening Assay

Cell Assay Seeding:

Briefly, clusters of H1 human embryonic stem cells were grown on reduced growth factor MATRIGEL™ (Invitrogen; Cat #356231)-coated tissue culture plastic. Cultures were treated with Accutase (Sigma; Cat #A6964), using equivalent volumes of 10 ml per 10 cm² surface area for 5 minutes at 37° C., then gently resuspended, pelleted by centrifugation, and resuspended in MEF conditioned medium for counting. For assay seeding, cells were plated at 50,000 cells/cm² on reduced growth factor MATRIGEL™-coated 96-well black plates (Packard ViewPlates; Cat #6005182) using volumes of 100 μl/well. Cells were allowed to attach and recover log phase growth over a 3 to 5 day period, feeding daily with MEF conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB). Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of assay.

Preparation of Compounds and Assay:

Stocks of EGF and FGF4 were prepared in a 96-well polypropylene plate (Corning, Inc.; Cat #3960). Compound 22 was available as a 5 mM stock solubilized in 100% DMSO (Sigma; Cat #D2650) and stored at −80° C. Assays were initiated by aspirating culture medium from each well followed by three washes in PBS to remove residual growth factors and serum. Test volumes of 80 μl per well were added back containing RPMI 1640 base medium (Invitrogen; Cat #22400-089) supplemented with 2.5% fatty acid free BSA (MP Biomedicals LLC; Cat #152401), 10 ng/ml bFGF (PeproTech Inc; Cat #100-18B), 25 ng/ml Wnt3a (R&D Systems; Cat #1324-WN) and 3.125 μM Compound 22 plus 20 μl 5× stock of growth factors to yield a final concentration of 2% fatty acid free BSA, 8 ng/ml bFGF (PeproTech Inc; Cat #100-18B), 20 ng/ml Wnt3a, and 2.5 μM Compound 22 in assay. Positive control wells contained the same base medium supplemented with 2% fatty acid free BSA, 8 ng/ml bFGF, 20 ng/ml Wnt3a, and 100 ng/ml recombinant human activin A (PeproTech; Cat #120-14). Negative control wells contained the same base medium supplemented with 2% fatty acid free BSA, 8 ng/ml bFGF, 20 ng/ml Wnt3a but omitted treatment with activin A.

On the second day of assay, wells were again aspirated and fed with 80 μl per well were added back containing RPMI 1640 base medium supplemented with 2.5% fatty acid free BSA, 10 ng/ml bFGF, and 3.125 μM Compound 22 plus 20 μl 5× stock of growth factors to yield a final concentration of 2% fatty acid free BSA, 8 ng/ml bFGF and 2.5 μM Compound 22 in assay. Positive control wells contained the same base medium supplemented with 2% fatty acid free BSA, 8 ng/ml bFGF and 100 ng/ml recombinant human activin A. Negative control samples contained the same base medium supplemented with 2% fatty acid free BSA and 8 ng/ml bFGF but omitted treatment with activin A.

High Content Analysis:

At the conclusion of four-days of culture, assay plates were washed twice with PBS, fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for one hour at room temperature. Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Molecular Probes; Cat #AZ1467) was diluted 1:200 in PBS and added to each sample well after washing three times with PBS. To counterstain nuclei, 4 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for ten minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Exposure times were optimized from positive control wells and from untreated negative control wells stained with secondary antibody alone. Images from 15 fields per well were acquired to compensate for any cell loss during the bioassay and subsequent staining procedures. Measurements for total cell number and total SOX17 intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria of gray-scale ranges between 200 to 3500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control. Normalized data were calculated for averages and standard deviations for each replicate set.

Table 10 shows results of this assay with Compound 34. Control samples with EGF and/or FGF4 alone without the Compound 34 had low SOX17 expression. Addition of Compound 34 added significant enhancement of SOX17 expression.

Example 11 A Comparison of the Ability of Activin a and GDF-8 to Differentiate Human Embryonic Stem Cells to Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage

A previous example showed that GDF-8 is able to replace activin A to differentiate human embryonic stem cells to cells expressing markers characteristic of the definitive endoderm lineage. It was important to know the relative potencies of GDF-8GDF-8 and activin A with respect their ability to differentiate human embryonic stem cells to cells expressing markers characteristic of the definitive endoderm lineage. A dose response assay was conducted using equivalent concentrations of each growth factor to compare results during embryonic stem cell differentiation.

Preparation of Cells for Assay:

Stock cultures of human embryonic stem cells (H1 human embryonic stem cell line) were maintained in an undifferentiated, pluripotent state on reduced growth factor MATRIGEL™-coated dishes in MEF conditioned medium with passage on average every four days. Passage was performed by exposing cell cultures to a solution of 1 mg/ml dispase (Invitrogen, Cat #: 17105-041) for 5 to 7 minutes at 37° C. followed by rinsing the monolayer with MEF conditioned culture medium and gentle scraping to recover cell clusters. Clusters were centrifuged at low speed to collect a cell pellet and remove residual dispase. Cell clusters were split at a 1:3 or 1:4 ratio for routine maintenance culture or a 1:1 ratio for immediate assay. All human embryonic stem cell lines were maintained at passage numbers less than 50 and routinely evaluated for normal karyotypic phenotype and for absence of mycoplasma contamination.

Cell clusters used in the assay were evenly resuspended in MEF conditioned medium supplemented with 8 ng/ml bFGF and seeded onto reduced growth factor MATRIGEL™-coated 96-well Packard VIEWPLATES (PerkinElmer; Cat #6005182) in volumes of 100 μl/well. MEF conditioned medium supplemented with 8 ng/ml bFGF was used for initial plating and expansion. Daily feeding was conducted by aspirating spent culture medium from each well and replacing with an equal volume of fresh medium. Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of assay.

Assay:

The assay was initiated by aspirating the culture medium from each well and adding back an aliquot (100 μl) of test medium. Test conditions were performed in quadruplicate over a total three-day assay period, feeding on day 1 and day 2 by aspirating and replacing the medium from each well with fresh test medium. Two 12-channel polypropylene basins (Argos technologies, Inc, Cat #: B3135) were used to make the test media containing different concentrations of Activin A (PeproTech; Cat #120-14) or GDF-8 (R&D Systems, Cat #788-G8). Channels numbered 2 through 12 of each basin contained 1 ml assay medium composed of RPMI-1640 medium (Invitrogen; Cat #: 22400) supplemented with 2% Albumin Bovine Fraction V, Fatty Acid Free (FAF BSA) (MP Biomedicals, Inc; Cat #152401) and 8 ng/ml bFGF (PeproTech Inc.; Cat #: 100-18B), and with 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN/CF) added on day 1, omitted on day 2 and 3. Channel number 1 of each basin contained 1600 ng/ml Activin A or 1600 ng/ml GDF-8, diluted into the same assay medium. One ml of medium was transferred from channel number 1 to channel number 2 and mixed well. A fresh pipette tip was used to transfer one ml of medium from channel number 2 to channel number 3, followed by thorough mixing. The same procedure was repeated in sequence through channel number 11 for each respective basin. Channel number 12 of each basin contained medium without Activin A or GDF-8. By doing this, a series of two-fold test dilutions was created, containing Activin A or GDF-8 at concentrations ranging from 1.6 ng/ml to 1600 ng/ml, for addition to the respective assay wells.

High Content Analysis:

At the conclusion of three days of culture, assay plates were washed once with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for two hours at room temperature. After washing three times with PBS, Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Invitrogen; Cat #A21467) diluted 1:200 in PBS was added to each well. To counterstain nuclei, 5 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for fifteen minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Images were acquired from 25 fields per well. Measurements for total SOX17 intensity in each well were obtained using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each quadruplicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by area of the cell. Background was eliminated based on acceptance criteria for gray-scale ranges between 200 to 4500. Total SOX17 intensity data were calculated using GraphPad Prism 4.02 (GraphPad Software, Inc., Lo Jolla, Calif.). Data were normalized to define the smallest and largest values in each data set as 0% and 100%, respectively. Table 11 shows the normalized values for each of the activin A and GDF-8 data sets. Two sigmoidal dose-response curves are shown in FIG. 2 as generated using the normalized values shown in Table 11. The R² values, indicating curve fit, were calculated using GraphPad Prism and determined to be 0.9944 for activin A and 0.9964 for GDF-8. Using GraphPad Prism, EC₅₀ values for each growth factor were calculated and determined to be 13.9 ng/ml for activin A and 184.8 ng/ml for GDF-8. These data indicate that GDF-8 is less potent than activin A with respect to inducing human embryonic stem cells to differentiate to cells expressing markers characteristic of the definitive endoderm lineage. Nonetheless, GDF-8 can substitute for activin A and at specific concentrations, can induce an equivalent population of definitive endoderm cells, as denoted by SOX17 expression.

Example 12 Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage that were Formed According to the Methods of the Present Invention are Able to Further Differentiate into Cells Expressing Markers Characteristic of the Pancreatic Endocrine Lineage

Parallel populations of human embryonic stem cells were differentiated to cells expressing markers characteristic of the definitive endoderm lineage using GDF-8 in combination with either Compound 34 or Compound 56. Thereafter, a step-wise differentiation protocol was applied to treated cells to promote differentiation toward pancreatic endoderm and endocrine lineages. A parallel control consisting of cells treated with Activin A and Wnt3a was maintained for comparison purposes throughout the step-wise differentiation process. Samples were taken at every stage of the differentiation to determine the appearance of proteins and mRNA biomarkers representative of the various stages of differentiation.

Preparation of Cells for Assay:

Stock cultures of human embryonic stem cells (H1 human embryonic stem cell line) were maintained in an undifferentiated, pluripotent state on reduced growth factor MATRIGEL™-coated dishes in MEF conditioned medium with passage on average every four days. Passage was performed by exposing cell cultures to a solution of 1 mg/ml dispase (Invitrogen; Cat #17105-041) for 5 to 7 minutes at 37° C. followed by rinsing the monolayer with MEF conditioned culture medium and gentle scraping to recover cell clusters. Clusters were centrifuged at low speed to collect a cell pellet and remove residual dispase. Cell clusters were split at a 1:3 or 1:4 ratio for routine maintenance culture or a 1:1 ratio for immediate assay. All human ES cell lines were maintained at passage numbers less than 50 and routinely evaluated for normal karyotype and absence of mycoplasma.

Cell clusters were evenly resuspended in MEF conditioned medium supplemented with 8 ng/ml bFGF and seeded onto reduced growth factor MATRIGEL™-coated 24-well, black wall culture plates (Arctic White; Cat #AWLS-303012) in volumes of 0.5 ml/well. Daily feeding was conducted by aspirating spent culture medium from each well and replacing with an equal volume of fresh medium. Plates were maintained at 37° C., 5% CO₂ throughout the duration of assay.

Assay:

The assay was initiated by aspirating the culture medium from each well and adding back an aliquot (0.5 ml) of test medium. Test conditions for the first step of differentiation were conducted over a three-day period, feeding daily by aspirating and replacing the medium from each well with fresh test medium. On the first day of assay, 100 ng/ml activin A (PeproTech; Cat #120-14) or 200 ng/ml GDF-8 (R&D Systems, Cat #788-G8) was added to respective assay wells where each growth factor was diluted into RPMI-1640 medium (Invitrogen; Cat #22400) with 1% Albumin Bovine Fraction V, Fatty Acid Free (FAF BSA) (MP Biomedicals, Inc; Cat #152401), 1% Probumin (Millipore; Cat #81-068-3) and 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN/CF). On the second day of assay, 100 ng/ml activin A or 200 ng/ml GDF-8 was diluted into RPMI-1640 medium supplemented with 2% FAF BSA without Wnt3a. In some test samples using GDF-8, Wnt3a was replaced with a either Compound 34 or Compound 56 at a concentration of 2.5 μM, and either Compound 34 or Compound 56 was added daily during all three days of definitive endoderm differentiation. At the conclusion of the first step of differentiation, cells from some wells were harvested for flow cytometry analysis to evaluate levels of CXCR4, a marker of definitive endoderm formation. Additional wells were harvested for RT-PCR analysis to measure other markers of differentiation.

At the conclusion of the first step of differentiation, replicate sets of parallel wells from each treatment group were subjected to further step-wise differentiation. It is important to note that after the first differentiation step, all wells undergoing continuing culture and differentiation received the same treatment. The protocol for this continuing differentiation is described below.

Step 2 of the differentiation protocol was carried out over two days. Cells were fed daily by aspirating the medium from each well and replacing with a fresh aliquot (0.5 ml) of DMEM:F12 medium (Invitrogen; Cat #11330-032) containing 2% Albumin Bovine Fraction V, Fatty Acid Free (FAF BSA) (MP Biomedicals, Inc; Cat #152401), 50 ng/ml FGF7 (PeproTech; Cat #100-19), and 250 nM cyclopamine (Calbiochem; Cat #239804).

Step 3 of the differentiation protocol was carried out over four days. Cells were fed daily by aspirating medium from each well and replacing with a fresh aliquot (0.5 ml) of DMEM-high glucose (Invitrogen; Cat #10569) supplemented with 1% B27 (Invitrogen; Cat #17504-044), 50 ng/ml FGF7, 100 ng/ml Noggin (R&D Systems; Cat #3344-NG), 250 nM KAAD-cyclopamine (Calbiochem; Cat #239804), and 2 μM all-trans retinoic acid (RA) (Sigma-Aldrich; Cat #R2625). At the conclusion of the third step of differentiation, cells from some wells were harvested for analysis by RT-PCR to measure markers of differentiation. Other culture wells were subjected to high content image analysis for protein expression levels of Pdx1, a transcription factor associated with pancreatic endoderm, and Cdx2, a transcription factor associated with intestinal endoderm.

Step 4 of the differentiation protocol was carried out over three days. Cells were fed daily by aspirating the medium from each well and replacing with a fresh aliquot (0.5 ml) of DMEM-high glucose supplemented with 1% B27, 100 ng/ml Noggin, 100 ng/ml Netrin-4, 1 μM DAPT (EMD Biosciences; Cat #565770), and 1 μM Alk 5 inhibitor (Axxora; Cat #ALX-270-445). At the conclusion of the fourth step of differentiation, cells from some wells were harvested for analysis by RT-PCR to measure markers of differentiation. Other culture wells were subjected to high content image analysis for protein expression levels of PDX1.

Step 5 of the differentiation protocol was carried out over seven days in DMEM-high glucose with 1% B27, and 1 μM Alk 5 inhibitor. Medium in each well was aspirated and replaced with a fresh aliquot (0.5 ml) on all days. At the conclusion of the fifth step of differentiation, cells from some wells were harvested for analysis by RT-PCR to measure markers of differentiation. Other culture wells were subjected to high content image analysis for protein expression levels of insulin and glucagon.

Step 6 of the differentiation protocol was carried out over seven days in DMEM-high glucose with 1% B27. Medium in each well was aspirated and replaced with a fresh aliquot (0.5 ml) on alternating days. At the conclusion of the sixth step of differentiation, cells from some wells were harvested for analysis by RT-PCR to measure markers of differentiation.

FACS Analysis:

Cells for FACS analysis were blocked in a 1:5 solution of 0.5% human gamma-globulin (Sigma; Cat #G-4386) in PBS (Invitrogen; Cat #14040-133): BD FACS staining buffer—BSA (BD; Cat #554657) for 15 minutes at 4° C. Cells were then stained with antibodies for CD9 PE (BD; Cat #555372), CD99 PE (Caltag; Cat #MHCD9904) and CXCR4 APC (R&D Systems; Cat #FAB173A) for 30 minutes at 4° C. After a series of washes in BD FACS staining buffer, the cells were stained for viability with 7-AAD (BD; Cat #559925) and run on a BD FACSArray. A mouse IgG1K Isotype control antibody for both PE and APC was used to gate percent positive cells.

RT-PCR Analysis:

RNA samples were purified by binding to a silica-gel membrane (Rneasy Mini Kit, Qiagen, CA) in the presence of an ethanol-containing, high-salt buffer followed by washing to remove contaminants. The RNA was further purified using a TURBO DNA-free kit (Ambion, INC), and high-quality RNA was then eluted in water. Yield and purity were assessed by A260 and A280 readings on a spectrophotometer. CDNA copies were made from purified RNA using an ABI (ABI, CA) high capacity cDNA archive kit.

Unless otherwise stated, all reagents were purchased from Applied Biosystems. Real-time PCR reactions were performed using the ABI PRISM® 7900 Sequence Detection System. TAQMAN® UNIVERSAL PCR MASTER MIX® (ABI, CA) was used with 20 ng of reverse transcribed RNA in a total reaction volume of 20 al. Each cDNA sample was run in duplicate to correct for pipetting errors. Primers and FAM-labeled TAQMAN®probes were used at concentrations of 200 nM. The level of expression for each target gene was normalized using a human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) endogenous control previously developed by Applied Biosystems. Primer and probe sets are listed in Table 12. After an initial incubation at 50° C. for 2 min followed by 95° C. for 10 min, samples were cycled 40 times in two stages—a denaturation step at 95° C. for 15 sec followed by an annealing/extension step at 60° C. for 1 min. Data analysis was carried out using GENEAMP®7000 Sequence Detection System software. For each primer/probe set, a Ct value was determined as the cycle number at which the fluorescence intensity reached a specific value in the middle of the exponential region of amplification. Relative gene expression levels were calculated using the comparative Ct method. Briefly, for each cDNA sample, the endogenous control Ct value was subtracted from the gene of interest Ct to give the delta Ct value (ΔCt). The normalized amount of target was calculated as 2−ΔCt, assuming amplification to be 100% efficiency. Final data were expressed relative to a calibrator sample.

High Content Analysis:

At the conclusion of culture, assay plates were washed once with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for two hours at room temperature. After washing three times with PBS, Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Invitrogen; Cat #A21467) diluted 1:200 in PBS was added to each well. To counterstain nuclei, 5 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for fifteen minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging. Other primary antibodies used for analysis included 1:100 dilution mouse anti-human CDX2 (Invitrogen; Cat #397800), 1:100 dilution goat anti-human Pdx1 (Santa Cruz Biotechnology; Cat #SC-14664), 1:200 dilution rabbit anti-human insulin (Cell Signaling; Cat #C27C9), and 1:1500 dilution mouse anti-human glucagon (Sigma-Aldrich; Cat #G2654). Secondary antibodies used for analysis included 1:400 dilution Alexa Fluor 647 chicken anti-mouse IgG (Invitrogen; Cat #A-21463), 1:200 dilution Alexa Fluor 488 donkey anti-goat IgG (Invitrogen; Cat #A11055), 1:1000 dilution Alexa Fluor 647 chicken anti-rabbit IgG (Invitrogen; Cat #A21443), and 1:1000 dilution Alexa Fluor 488 chicken anti-mouse IgG (Invitrogen; Cat #A21200).

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Images were acquired from 25 fields per well. Measurements for total intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria for gray-scale ranges between 200 and 4500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control.

PCR results for representative differentiation markers are shown in Table 13 for cells harvested from each step of differentiation. Samples treated with GDF-8 and Wnt3a or with GDF-8 and either Compound 34 or Compound 56 showed similar, or in some instances, improved expression levels of expression markers associated with endodermal and endocrine differentiation.

FIG. 3 shows the results of the FACS analysis, showing the expression of the definitive endoderm marker, CXCR4, after the first step of differentiation. Treatment of human embryonic stem cells with GDF-8 and Wnt3a yielded an equivalent percentage of CXCR4 positive cells compared to treatment with activin A and Wnt3a. Similarly, treatment of human embryonic stem cells with GDF-8 and a small molecule (Compound 34 or Compound 56) also yielded an equivalent or higher percentage of CXCR4 positive cells. FIG. 4 shows high content image analysis for normalized SOX17 protein expression in human embryonic stem cells after three days differentiation to definitive endoderm. Levels of expression for treatment groups using GDF-8 with Wnt3a or GDF-8 with a small molecule are similar to treatment with Activin A and Wnt3a.

FIG. 5 shows high content image analysis for normalized Pdx1 and Cdx2 protein expression in human embryonic stem cells after the third step of differentiation to pancreatic endoderm. Levels of expression for treatment groups using GDF-8 with Wnt3a or GDF-8 with Wnt3a or GDF-8 with a compound of the present invention show equivalent levels of PDX1 and CDX2. In some treatment groups the cell number retained after differentiation decreased thereby increasing the ratio of PDX1 expressing cells. Similar results were obtained showing equivalent normalized PDX1 expression in all treatment groups after the fourth step of differentiation as shown in FIG. 6. In FIG. 7, normalized protein levels of insulin and glucagon are shown, demonstrating equivalent expression between the Activin A and GDF-8 treatment groups.

These collective results demonstrate that GDF-8, in combination with Wnt3a or Compound 34 or Compound 56, can substitute for activin A during definitive endoderm differentiation and subsequent pancreatic endoderm and endocrine differentiation.

Example 13 Formation of Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage with Other Members of the GDF Family of Proteins

It was important to determine if treating human embryonic stem cells with other GDF family members could the formation of cells expressing markers characteristic of the definitive endoderm lineage. Wnt3a in combination with either Compound 34 or Compound 56 were tested on human embryonic stem cells in combination with six different GDF growth factors [GDF-3, GDF-5, GDF-8, GDF-10, GDF-11, and GDF-15] to determine the ability of members of the GDF family of proteins to differentiate human embryonic stem cells toward cells expressing markers characteristic of the definitive endoderm lineage. A parallel control of cells treated with activin A and Wnt3a was maintained for comparison purposes.

Preparation of Cells for Assay:

Stock cultures of human embryonic stem cells (H1 human embryonic stem cell line) were maintained in an undifferentiated, pluripotent state on reduced growth factor MATRIGEL™ (BD Biosciences; Cat #356231)-coated dishes in MEF conditioned medium with passage on average every four days. Passage was performed by exposing cell cultures to a solution of 1 mg/ml dispase (Invitrogen; Cat #17105-041) for 5 to 7 minutes at 37° C. followed by rinsing the monolayer with MEF conditioned culture medium and gentle scraping to recover cell clusters. Clusters were centrifuged at low speed to collect a cell pellet and remove residual dispase. Cell clusters were split at a 1:3 or 1:4 ratio for routine maintenance culture or a 1:1 ratio for immediate assay. All human ES cell lines were maintained at passage numbers less than 50 and routinely evaluated for normal karyotype and absence of mycoplasma.

Cell clusters were evenly resuspended in MEF conditioned medium supplemented with 8 ng/ml bFGF and seeded onto reduced growth factor MATRIGEL™-coated 96-well Packard VIEWPLATES (PerkinElmer; Cat #6005182) in volumes of 0.1 ml/well. Daily feeding was conducted by aspirating spent culture medium from each well and replacing with an equal volume of fresh medium. Plates were maintained at 37° C., 5% CO₂ throughout the duration of assay.

Assay:

The assay was initiated by aspirating the culture medium from each well and adding back aliquots (100 μl) of test medium. Test conditions were performed in triplicate over a total four-day assay period, feeding on day 1 and day 3 by aspirating and replacing the medium from each well with fresh test medium. Various members of the GDF family of proteins were obtained for testing as follows: GDF-3 (PeproTech; Cat #120-22); GDF-5 (DePuy Orthopaedics, Inc., a Johnson & Johnson company); GDF-8 (R&D Systems; Cat #788-G8); GDF-10 (R&D Systems; Cat #1543-BP); GDF-11 (PeproTech; Cat #120-11); GDF-15 (R&D Systems; Cat #957-GD). On the first day of assay, all wells received an aliquot (80 μl) of basal medium DMEM:F12 medium (Invitrogen; Cat #11330-032) supplemented with 0.5% fetal bovine serum (Hyclone; Cat #SH30070.03). A series of five different control or experimental test samples was created to evaluate activin A or various GDFs in combination with Wnt3a or Compound 34 or Compound 56. These test samples were added in 20 μl aliquots (5× concentrated) to appropriately matched assay wells to yield a final assay volume of 100 μl in each well at the final assay conditions indicated. In the first set of control samples, the following conditions were tested: 1) no additive (i.e. no supplementary growth factor or small molecule); 2) 100 ng/ml activin A (PeproTech; Cat #120-14) in combination with 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN/CF); 3) 20 ng/ml Wnt3a alone; 4) Compound 34 alone (2.5 μM) without any growth factor or small molecule; 5) Compound 56 alone (2.5 μM) without any growth factor or small molecule. In the second set of test samples, the following conditions were tested in combination with 100 ng/ml GDF-3: 1) no additive (i.e. GDF-3 alone); 2) 20 ng/ml Wnt3a; 3) 20 ng/ml Wnt3a with Compound 34 (2.5 μM); 4) Compound 34 (2.5 μM); 5) Compound 56 (2.5 μM); and 6) 20 ng/ml Wnt3a with Compound 56 (2.5 μM). In the third set of test samples, each of the six conditions was combined with 100 ng/ml GDF-5. In the fourth set of test samples, each of the six conditions was combined with 100 ng/ml GDF-8. In the fifth set of test samples, each of the six conditions was combined with 100 ng/ml GDF-10. In the sixth set of test samples, each of the six conditions was combined with 100 ng/ml GDF-11. In the seventh set of test samples, each of the six conditions was combined with 100 ng/ml GDF-15. On the third day of assay, all wells for all test samples, received 100 ng/ml Activin A or 100 ng/ml respective GDF growth factor, without Wnt3a or Compound 34 or Compound 56, diluted into DMEM:F12 medium supplemented with 2% FBS.

High Content Analysis:

At the conclusion of culture, assay plates were washed once with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for two hours at room temperature. After washing three times with PBS, Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Invitrogen; Cat #A21467) diluted 1:200 in PBS was added to each well. To counterstain nuclei, 5 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for fifteen minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Images were acquired from 25 fields per well. Measurements for total intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria for gray-scale ranges between 200 and 4500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control.

FIG. 8 shows high content image analysis for SOX17 protein expression in human embryonic stem cells after four days differentiation to definitive endoderm. In each case, results are normalized to the positive control treatment with activin A and Wnt3a. In FIG. 8A, only the positive control treatment yielded significant expression of SOX17; treatment with Wnt3a alone or either Compound 34 or Compound 56 alone failed to induce SOX17 expression. In FIG. 8B through FIG. 8G, normalized SOX17 expression levels are shown for each GDF growth factor substituting for activin A in the respective treatments. GDF-3 (FIG. 8B) and GDF-5 (FIG. 8C) induced weak expression of SOX17 and only in test samples where one of the compounds of the present invention was present. GDF10 (FIG. 8D), GDF-11 (FIG. 8E) and GDF-15 (FIG. 8G) induced significant levels of SOX17 expression, more than observed with GDF-3 or 5 treatments but less than observed that observed with activin A and Wnt3a treatment. In general, SOX17 expression was negligible when GDF-10, GDF-11, or GDF-15 was combined with Wnt3a, but improved in combination with one of the compounds of the present invention; in particular when combined with Compound 34. FIG. 8D shows results for treatment groups using GDF-8 where GDF-8 in combination with either Compound 34 or Compound 56 caused a robust induction of SOX17, exceeding results seen with the activin A/Wnt3a positive control. In some of these examples, the presence of Compound 34 or Compound 56 combined with a GDF growth factor also caused an increase in cell number during differentiation.

These collective results demonstrate that GDF-8 was superior to all other GDF family members tested when used in combination with Compound 34 or Compound 56, and could substitute for activin A during definitive endoderm differentiation.

Example 14 Formation of Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage with Other Members of the TGF Superfamily of Proteins

It was important to determine if treating human embryonic stem cells with other TGF superfamily members could facilitate the formation of cells expressing markers characteristic of the definitive endoderm lineage. Compound 34 and Wnt3a were tested on human embryonic stem cells in combination with either TGFβ-1, BMP2, BMP3, or BMP4 to determine the ability of members of the TGF superfamily members to differentiate human embryonic stem cells toward cells expressing markers characteristic of the definitive endoderm lineage. In parallel, two different commercial sources of GDF-8 were tested with Wnt3a for their ability to differentiate human embryonic stem cells toward cells expressing markers characteristic of the definitive endoderm lineage. A positive control using activin A with Wnt3a was maintained for comparison purposes.

Preparation of Cells for Assay:

Stock cultures of human embryonic stem cells (H1 human embryonic stem cell line) were maintained in an undifferentiated, pluripotent state on reduced growth factor MATRIGEL™-(BD Biosciences; Cat #356231)-coated dishes in MEF conditioned medium with passage on average every four days. Passage was performed by exposing cell cultures to a solution of 1 mg/ml dispase (Invitrogen; Cat #17105-041) for 5 to 7 minutes at 37° C. followed by rinsing the monolayer with MEF conditioned culture medium and gentle scraping to recover cell clusters. Clusters were centrifuged at low speed to collect a cell pellet and remove residual dispase. Cell clusters were split at a 1:3 or 1:4 ratio for routine maintenance culture or a 1:1 ratio for immediate assay. All human embryonic stem cell lines were maintained at passage numbers less than 50 and routinely evaluated for normal karyotype and absence of mycoplasma.

Cell clusters were evenly resuspended in MEF conditioned medium supplemented with 8 ng/ml bFGF and seeded onto reduced growth factor MATRIGEL™-coated 96-well Packard VIEWPLATES (PerkinElmer; Cat #6005182) in volumes of 0.1 ml/well. Daily feeding was conducted by aspirating spent culture medium from each well and replacing with an equal volume of fresh medium. Plates were maintained at 37° C., 5% CO₂ throughout assay.

Assay:

The assay was initiated by aspirating the culture medium from each well and adding back aliquots (100 μl) of test medium. Test conditions were performed in triplicate over a total three day assay period, feeding on day 1 and day 2 by aspirating and replacing the medium from each well with fresh test medium. Various growth factor proteins were obtained for testing as follows: BMP-2 (R&D Systems; Cat #355-BM); BMP-3 (R&D Systems; Cat #113-BP); BMP-4 (R&D Systems; Cat #314-BP); TGFβ-1 (R&D Systems; Cat #240-B); GDF-8 (PeproTech; Cat #120-00); GDF-8 (Shenandoah; Cat #100-22); and activin A (PeproTech; Cat #120-14). On the first day of assay, each well was treated with 80 μl of growth medium [RPMI-1640 (Invitrogen; Cat #: 22400) containing 2.5% Albumin Bovine Fraction V, Fatty Acid Free (FAF BSA) (MP Biomedicals, Inc; Cat #152401), and 10 ng/ml bFGF]. In some wells, 25 ng/ml Wnt3a (R&D Systems; Cat #1324-WN/CF) was added to the growth medium to yield a final assay concentration of 20 ng/ml. In some wells, activin A was added to the growth medium to yield a final assay concentration of 100 ng/ml. In some wells, 3.125 μM Compound 34 was added to the growth medium to yield a final assay concentration of 2.5 μM. A dose titration of additional growth factors (5× concentrated, diluted in RPMI-1640) was also added to respective test wells to yield a final assay volume of 100 μl in each well for all treatment conditions. On the second day of assay, Wnt3a and Compound 34 were omitted from assay. All wells received 80 μl of growth medium (RPMI-1640 containing 2.5% FAF BSA, and 10 ng/ml bFGF) and 20 μl of respective growth factor dilution (5× concentrated, diluted in RPMI-1640). Comparative controls for this assay included: 1) no added growth factors; 2) Wnt3a alone; and 3) activin A with Wnt3a. Each commercial source of GDF-8 was tested in combination with Wnt3a. Each of the BMP growth factors, as well as TGFβ-1, was tested in combination with Wnt3a, with Compound 34, and with both Wnt3a in combination with Compound 34.

High Content Analysis:

At the conclusion of culture, assay plates were washed once with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for two hours at room temperature. After washing three times with PBS, Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Invitrogen; Cat #A21467) diluted 1:200 in PBS was added to each well. To counterstain nuclei, 5 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for fifteen minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Images were acquired from 25 fields per well. Measurements for total intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria for gray-scale ranges between 200 and 4500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control.

FIG. 9A to FIG. 9G show high content image analysis for SOX17 protein expression in human embryonic stem cells after three days differentiation to definitive endoderm. In each case, results are normalized to the positive control treatment for activin A with Wnt3a. The results in FIG. 9A show that treatment with growth medium alone, or Wnt3a alone failed to induce SOX17 expression; only the addition of activin A caused a robust expression of SOX17. In FIG. 9B and FIG. 9C results for each of the commercial sources of GDF-8 are depicted, showing differences in potency between the two vendors. Although less potent than activin A, there was significant induction of SOX17 expression in cells treated with GDF-8 in combination with Wnt3a. In FIG. 9D to FIG. 9G, results are shown for definitive endoderm differentiation using BMP2, BMP3, BMP4, and TGFβ-1, incorporating a dose titration for each growth factor in combination with Wnt3a, or Compound 34, or both Wnt3a with Compound 34. Although some treatments had a significant effect on cell numbers at the conclusion of assay (e.g. BMP2 and BMP4), induction of SOX17 expression resulting from any of these growth factors and treatment combinations was weak or negligible compared to the Wnt3a treatment alone.

Example 15 Dose Ranging Studies for Formation of Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage with a Selection of the Compounds of the Present Invention

It was important to know the optimal working concentrations for Compound 181, Compound 180, Compound 19, Compound 202, Compound 40, and Compound 34 that would mediate the formation of cells expressing markers characteristic of the definitive endoderm lineage. In conjunction, side-by-side comparisons were performed for titrations of each compound in combination with activin A or GDF-8 in the definitive endoderm assay. Finally, the duration of exposure for each compound was tested in assay, also in combination with activin A or GDF-8, adding compound only on the first day of assay or throughout all three days of definitive endoderm formation.

Preparation of Cells for Assay:

Stock cultures of human embryonic stem cells (H1 human embryonic stem cell line) were maintained in an undifferentiated, pluripotent state on reduced growth factor MATRIGEL™ (BD Biosciences; Cat #356231)-coated dishes in MEF conditioned medium supplemented with 8 ng/ml bFGF (PeproTech Inc.; Cat #100-18B) with passage on average every four days. Passage was performed by exposing cell cultures to a solution of 1 mg/ml dispase (Invitrogen; Cat #17105-041) for 5 to 7 minutes at 37° C. followed by rinsing the monolayer with MEF conditioned culture medium and gentle scraping to recover cell clusters. Clusters were centrifuged at low speed to collect a cell pellet and remove residual dispase. Cell clusters were split at a 1:3 or 1:4 ratio for routine maintenance culture or a 1:1 ratio for immediate assay. All human embryonic stem cell lines were maintained at passage numbers less than 50 and routinely evaluated for normal karyotype and absence of mycoplasma.

Cell clusters were evenly resuspended in MEF conditioned medium supplemented with 8 ng/ml bFGF and seeded onto reduced growth factor MATRIGEL™-coated 96-well Packard VIEWPLATES (PerkinElmer; Cat #6005182) in volumes of 0.1 ml/well. Daily feeding was conducted by aspirating spent culture medium from each well and replacing with an equal volume of fresh medium. Plates were maintained at 37° C., 5% CO₂ throughout the duration of assay.

Assay:

Assay was initiated by aspirating the culture medium from each well and adding back aliquots (100 μl) of test medium. Test conditions were performed in quadruplicate over a total four-day assay period, feeding daily by aspirating and replacing the medium from each well with fresh test medium. Each well was treated with 80 μl of growth medium [RPMI-1640 (Invitrogen; Cat #: 22400) containing 2.5% Albumin Bovine Fraction V, Fatty Acid Free (FAF BSA) (MP Biomedicals, Inc; Cat #152401), 10 ng/ml bFGF, and additional growth factors (1.25× concentrated)] and 20 μl of test compound (5× concentrated diluted in RPMI-1640) to yield a final assay volume of 100 ul in each well. Test compounds in this assay included six of the compounds of the present invention: Compound 181, Compound 180, Compound 19, Compound 202, Compound 40, and Compound 34, and a commercial GSK3i inhibitor BIO (EMD Chemicals, Inc.; Cat #361550). On the first day of assay, wells were treated with various control or experimental conditions. Control conditions, with final assay concentrations as indicated, were as follows: 1) growth medium alone; 2) 20 ng/ml Wnt3a only R&D Systems; Cat #1324-WN/CF); 3) 100 ng/ml activin A (PeproTech; Cat #120-14); 4) 100 ng/ml activin A and 20 ng/ml Wnt3a; 5) 100 ng/ml GDF-8 (R&D Systems, Cat #788-G8); 6) 100 ng/ml GDF-8 and 20 ng/ml Wnt3a. Test compounds were diluted two-fold in series to yield a concentration range from 78 nM to 10 μM in the final assay. Experimental test samples combined each individual compound dilution series with 100 ng/ml activin A or 100 ng/ml GDF-8, both treatment sets in the absence of Wnt3a. On the second and third day of assay, some wells continued to be treated with 20 ng/ml Wnt3a or diluted test compound in combination with either activin A or GDF-8. In other wells, activin A or GDF-8 treatment continued on the second and third day of assay, but Wnt3a or diluted test compound was removed.

High Content Analysis:

At the conclusion of culture, assay plates were washed once with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for two hours at room temperature. After washing three times with PBS, Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Invitrogen; Cat #A21467) diluted 1:200 in PBS was added to each well. To counterstain nuclei, 5 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for fifteen minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Images were acquired from 25 fields per well. Measurements for total intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria for gray-scale ranges between 200 and 4500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control.

Results:

High content analysis results are shown for SOX17 expression in FIGS. 10-14G and resulting cell number at the conclusion of assay in FIGS. 15-19G. In FIG. 10, results are shown for SOX 17 expression resulting from control treatments using activin A or GDF-8, either alone or in combination with Wnt3a. Activin A treatments resulted in significantly higher SOX17 expression than was observed with GDF-8 treatment. Similarly, as seen in FIG. 15, activin A treatment resulted in a higher number of cells at the conclusion of assay than was seen with GDF-8 treatment, regardless of whether Wnt3a was present for one or three days during assay. Adding any of Compound 181, Compound 180, Compound 19, Compound 202, Compound 40, or Compound 34 with activin A treatment did not enhance SOX 17 expression (FIGS. 11A-12G) or increase cell numbers (FIGS. 17A-18G), regardless of whether the compound was present for one day at the initiation of assay or three days throughout the duration of assay. However, treatment with either Compound 181, Compound 180, Compound 19, Compound 202, Compound 40, or Compound 34 in combination with GDF-8 significantly improved SOX17 expression (FIGS. 13A-14G) and also enhanced cell numbers at the end of assay (FIGS. 18A-19G). When either Compound 181, Compound 180, Compound 19, Compound 202, Compound 40, or Compound 34 and GDF-8 were used in combination, the improvements to SOX17 expression and cell number in many cases were equivalent to results observed with activin A treatment. Improved differentiation in combination with GDF-8 was apparent in a dose titration effect for many of the compounds, although toxicity was sometimes observed at the highest concentrations. In most cases, optimal beneficial effects from treatment with the compound and GDF-8 were apparent with only one day of compound exposure at the initiation of assay. In some cases, presence of the compound throughout the duration of assay had no detrimental effect or had a slight beneficial effect. From these collective results an optimal working concentration range for each compound in combination with GDF-8 treatment was determined. Results were compound specific, generally in the 1-10 μM range as tested in this assay.

Example 16 Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage that were Formed without According to the Methods of the Present Invention are Able to Further Differentiate into Cells Expressing Markers Characteristic of the Pancreatic Endocrine Lineage

Additional small molecules were tested in combination with GDF-8 for definitive endoderm differentiation. These included a commercial inhibitor of GSK3 as well as compounds of the present invention. A step-wise differentiation protocol was applied to cells treated with GDF-8 in combination with various small molecules. The efficacy of differentiation was determined by gene expression for biomarkers representative the pancreatic endoderm, or pancreatic endocrine lineages. A parallel control sample of cells treated with activin A and Wnt3a was maintained for comparison purposes throughout the step-wise differentiation process.

Preparation of Cells for Assay:

Stock cultures of human embryonic stem cells (H1 human embryonic stem cell line) were maintained in an undifferentiated, pluripotent state on reduced growth factor MATRIGEL™ (BD Biosciences; Cat #356231)-coated dishes in MEF conditioned medium with passage on average every four days. Passage was performed by exposing cell cultures to a solution of 1 mg/ml dispase (Invitrogen, Cat #: 17105-041) for 5 to 7 minutes at 37° C. followed by rinsing the monolayer with MEF conditioned culture medium and gentle scraping to recover cell clusters. Clusters were centrifuged at low speed to collect a cell pellet and remove residual dispase. Cell clusters were split at a 1:3 or 1:4 ratio for routine maintenance culture or a 1:1 ratio for immediate assay. All human embryonic stem cell lines were maintained at passage numbers less than 50 and routinely evaluated for normal karyotype and absence of mycoplasma.

Cell clusters were evenly resuspended in MEF conditioned medium supplemented with 8 ng/ml bFGF and plated onto reduced growth factor MATRIGEL-coated 24-well, black wall culture plates (Arctic White; Cat #AWLS-303012) in volumes of 0.5 ml/well. Daily feeding was conducted by aspirating spent culture medium from each well and replacing with an equal volume of fresh medium. Plates were maintained at 37° C., 5% CO₂ throughout the duration of assay.

Assay:

The assay was initiated by aspirating the culture medium from each well and adding back an aliquot (0.5 ml) of test medium. Test conditions for the first step of differentiation were conducted over a three-day period, feeding daily by aspirating and replacing the medium from each well with fresh test medium. On the first day of assay, 100 ng/ml activin A (PeproTech; Cat #120-14) or 100 ng/ml GDF-8 (R&D Systems, Cat #788-G8) was added to respective assay wells where each growth factor was diluted into RPMI-1640 medium (Invitrogen; Cat #: 22400) with 2% Albumin Bovine Fraction V, Fatty Acid Free (FAF BSA) (Proliant Inc. Cat #: SKU 68700), and 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN/CF). On the second day of assay, 100 ng/ml activin A or 100 ng/ml GDF-8 was diluted into RPMI-1640 medium supplemented with 2% FAF BSA without Wnt3a. In some test samples using GDF-8, Wnt3a was replaced with a small molecule compound, added only on the first day of definitive endoderm differentiation. These small molecules included Compound 19 (2.5 μM in assay), Compound 202 (2.5 μM in assay), Compound 40 (2.5 μM in assay), or a commercially available GSK3 inhibitor BIO (0.5 μM in assay) (EMD Chemicals, Inc.; Cat #361550). At the conclusion of the first step of differentiation, cells from some wells were harvested for flow cytometry analysis to evaluate levels of CXCR4, a marker of definitive endoderm formation. Additional wells were harvested for RT-PCR analysis to measure other markers of differentiation.

At the conclusion of the first step of definitive endoderm differentiation, replicate sets of parallel wells from each treatment group were subjected to further step-wise differentiation. It is important to note that after the first differentiation step, all wells undergoing subsequent culture and differentiation received the same treatment. The protocol for this continuing differentiation is described below.

Step 2 of the differentiation protocol was carried out over two days. Cells were fed daily by aspirating the medium from each well and replacing with a fresh aliquot (0.5 ml) of DMEM:F12 medium (Invitrogen; Cat #11330-032) containing 2% FAF BSA, 50 ng/ml FGF7 (PeproTech; Cat #100-19), and 250 nM cyclopamine-KAAD (Calbiochem; Cat #239804).

Step 3 of the differentiation protocol was carried out over seven days. Cells were fed daily by aspirating medium from each well and replacing with a fresh aliquot (0.5 ml) of DMEM-high glucose (Invitrogen; Cat #10569) supplemented with 0.1% Albumax (Invitrogen; Cat #: 11020-021), 0.5× Insulin-Transferrin-Selenium (ITS-X; Invitrogen; Cat #51500056), 50 ng/ml FGF7, 100 ng/ml Noggin (R&D Systems; Cat #3344-NG), 250 nM KAAD-cyclopamine, and 2 μM all-trans retinoic acid (RA) (Sigma-Aldrich; Cat #R2625). At the conclusion of the third step of differentiation, cells from some wells were harvested for analysis by RT-PCR to measure markers of differentiation. Other culture wells were subjected to high content image analysis for protein expression levels of Pdx1, and Cdx2.

Step 4 of the differentiation protocol was carried out over three days. Cells were fed daily by aspirating the medium from each well and replacing with a fresh aliquot (0.5 ml) of DMEM-high glucose supplemented with 0.1% Albumax, 0.5× Insulin-Transferrin-Selenium, 100 ng/ml Noggin, and 1 μM Alk 5 inhibitor (Axxora; Cat #ALX-270-445). At the conclusion of the fourth step of differentiation, cells from some wells were harvested for analysis by RT-PCR to measure markers of differentiation. Other culture wells were subjected to high content image analysis for protein expression levels of Pdx1.

Step 5 of the differentiation protocol was carried out over seven days in DMEM-high glucose with 0.1% Albumax, 0.5× Insulin-Transferrin-Selenium, and 1 μM Alk 5 inhibitor. Medium in each well was aspirated and replaced with a fresh aliquot (0.5 ml) on all days. At the conclusion of the fifth step of differentiation, cells from some wells were harvested for analysis by RT-PCR to measure markers of differentiation. Other culture wells were subjected to high content image analysis for protein expression levels of insulin and glucagon.

FACS Analysis:

Cells for FACS analysis were blocked in a 1:5 solution of 0.5% human gamma-globulin (Sigma; Cat #G-4386) in PBS (Invitrogen; Cat #14040-133): BD FACS staining buffer—BSA (BD; Cat #554657) for 15 minutes at 4° C. Cells were then stained with antibodies for CD9 PE (BD; Cat #555372), CD99 PE (Caltag; Cat #MHCD9904) and CXCR4 APC (R&D Systems; Cat #FAB173A) for 30 minutes at 4° C. After a series of washes in BD FACS staining buffer, the cells were stained for viability with 7-AAD (BD; Cat #559925) and run on a BD FACSArray. A mouse IgG1K Isotype control antibody for both PE and APC was used to gate percent positive cells.

RT-PCR Analysis:

RNA samples were purified by binding to a silica-gel membrane (Rneasy Mini Kit, Qiagen, CA) in the presence of an ethanol-containing, high-salt buffer followed by washing to remove contaminants. The RNA was further purified using a TURBO DNA-free kit (Ambion, INC), and high-quality RNA was then eluted in water. Yield and purity were assessed by A260 and A280 readings on a spectrophotometer. CDNA copies were made from purified RNA using an ABI (ABI, CA) high capacity cDNA archive kit.

Unless otherwise stated, all reagents were purchased from Applied Biosystems. Real-time PCR reactions were performed using the ABI PRISM® 7900 Sequence Detection System. TAQMAN® UNIVERSAL PCR MASTER MIX® (ABI, CA) was used with 20 ng of reverse transcribed RNA in a total reaction volume of 20 μl. Each cDNA sample was run in duplicate to correct for pipetting errors. Primers and FAM-labeled TAQMAN®probes were used at concentrations of 200 nM. The level of expression for each target gene was normalized using a human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) endogenous control previously developed by Applied Biosystems. Primer and probe sets are listed in Table 12. After an initial incubation at 50° C. for 2 min followed by 95° C. for 10 min, samples were cycled 40 times in two stages—a denaturation step at 95° C. for 15 sec followed by an annealing/extension step at 60° C. for 1 min. Data analysis was carried out using GENEAMP®7000 Sequence Detection System software. For each primer/probe set, a Ct value was determined as the cycle number at which the fluorescence intensity reached a specific value in the middle of the exponential region of amplification. Relative gene expression levels were calculated using the comparative Ct method. Briefly, for each cDNA sample, the endogenous control Ct value was subtracted from the gene of interest Ct to give the delta Ct value (ΔCt). The normalized amount of target was calculated as 2−ΔCt, assuming amplification to be 100% efficiency. Final data were expressed relative to a calibrator sample.

High Content Analysis:

At the conclusion of culture, assay plates were washed once with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for two hours at room temperature. After washing three times with PBS, Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Invitrogen; Cat #A21467) diluted 1:200 in PBS was added to each well. To counterstain nuclei, 5 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for fifteen minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging. Other primary antibodies used for analysis included 1:200 dilution rabbit anti-human insulin (Cell Signaling; Cat #C27C9), and 1:1500 dilution mouse anti-human glucagon (Sigma-Aldrich; Cat #G2654). Secondary antibodies used for analysis included 1:1000 dilution Alexa Fluor 647 chicken anti-rabbit IgG (Invitrogen; Cat #A21443), and 1:1000 dilution Alexa Fluor 488 chicken anti-mouse IgG (Invitrogen; Cat #A21200).

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Images were acquired from 25 fields per well. Measurements for total intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria for gray-scale ranges between 200 and 4500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control.

PCR results for representative differentiation markers are shown in Table 14 for cells harvested from each step of differentiation. Samples treated with GDF-8 and Wnt3a or with GDF-8 and a small molecule showed similar expression levels of markers associated with endodermal and endocrine differentiation.

FIG. 20A shows FACS analysis for the definitive endoderm marker, CXCR4, after the first step of differentiation. Treatment of human embryonic stem cells with GDF-8 and Wnt3a yielded a similar percentage of CXCR4 positive cells compared to treatment with activin A and Wnt3a. Treatment of human embryonic stem cells with GDF-8 and a compound of the present invention (Compound 19, Compound 202, Compound 40, or GSK3 inhibitor IX BIO) also yielded an equivalent or slightly higher percentage of CXCR4 positive cells. FIG. 20B shows high content image analysis for normalized SOX17 protein expression in human embryonic stem cells after three days differentiation to definitive endoderm. In some cases, treatment with GDF-8 resulted in a lower cell number at the conclusion of the first step of differentiation. However, GDF-8 treatment in combination with Wnt3a or with the small molecule inhibitors clearly induced expression of SOX17, a marker of definitive endoderm. In one instance, treatment with GDF-8 and Compound 40 yielded cell numbers in culture and SOX17 expression equivalent to treatment with activin A and Wnt3a.

FIG. 20C shows high content image analysis for relative cell numbers recovered from cultures treated through differentiation step 5. As observed earlier at the end of step 1, some treatments caused a drop in cell recovery relative to treatment with activin A and Wnt3a. This decrease in cell number was seen specifically with treatment groups using GDF-8 with GSK3 inhibitor BIO and also using GDF-8 with Compound 19. Additional GDF-8 treatment groups had cell recoveries similar to treatment with activin A and Wnt3a. In FIG. 20D to FIG. 20F, normalized protein levels of insulin and glucagon are shown, along with their respective ratio for each treatment group. Similar levels of insulin and glucagon could be obtained with each of the GDF-8 treatments relative to treatment with activin A and Wnt3a, demonstrating that GDF-8, in combination with Wnt3a or a small molecule, can substitute for activin A during definitive endoderm differentiation and subsequent pancreatic endoderm and endocrine differentiation.

Example 17 Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage that were Formed Using GDF-8 and a Compound of the Present Invention are Able to Further Differentiate into Cells Expressing Markers Characteristic of the Pancreatic Endocrine Lineage

Additional small molecules were tested in combination with GDF-8 and activin A for definitive endoderm differentiation. These included a commercial inhibitor of GSK3 as well as the compounds of the present invention. A step-wise differentiation protocol was applied to cells treated with GDF-8 in combination with various small molecules. The efficacy of differentiation was determined by gene expression for biomarkers representative of the pancreatic endoderm and pancreatic endocrine lineages. A parallel control sample of cells treated with activin A and Wnt3a was maintained for comparison purposes throughout the step-wise differentiation process.

Preparation of Cells for Assay:

Stock cultures of human embryonic stem cells (H1 human embryonic stem cell line) were maintained in an undifferentiated, pluripotent state on reduced growth factor MATRIGEL™ (BD Biosciences; Cat #356231)-coated dishes in MEF conditioned medium supplemented with 8 ng/ml bFGF (PeproTech Inc.; Cat #100-18B) with passage on average every four days. Passage was performed by exposing cell cultures to a solution of 1 mg/ml dispase (Invitrogen; Cat #17105-041) for 5 to 7 minutes at 37° C. followed by rinsing the monolayer with MEF conditioned culture medium and gentle scraping to recover cell clusters. Clusters were centrifuged at low speed to collect a cell pellet and remove residual dispase. Cell clusters were split at a 1:3 or 1:4 ratio for routine maintenance culture or a 1:1 ratio for immediate assay. All human ES cell lines were maintained at passage numbers less than 50 and routinely evaluated for normal karyotype and absence of mycoplasma.

Cell clusters were evenly resuspended in MEF conditioned medium supplemented with 8 ng/ml bFGF and plated onto reduced growth factor MATRIGEL™-coated 24-well, black wall culture plates (Arctic White; Cat #AWLS-303012) in volumes of 0.5 ml/well. Daily feeding was conducted by aspirating spent culture medium from each well and replacing with an equal volume of fresh medium. Plates were maintained at 37° C., 5% CO₂ throughout assay.

Assay:

The assay was initiated by aspirating the culture medium from each well and adding back an aliquot (0.5 ml) of test medium. Test conditions for the first step of differentiation were conducted over a three-day period, feeding daily by aspirating and replacing the medium from each well with fresh test medium. On the first day of assay, 100 ng/ml activin A (PeproTech; Cat #120-14) or 100 ng/ml GDF-8 (R&D Systems, Cat #788-G8) was added to respective assay wells where each growth factor was diluted into RPMI-1640 medium (Invitrogen; Cat #: 22400) with 2% Albumin Bovine Fraction V, Fatty Acid Free (FAF BSA) (MP Biomedicals, Inc; Cat #152401). In some samples, 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN/CF) was also included. On the second day of assay, 100 ng/ml activin A or 100 ng/ml GDF-8 was diluted into RPMI-1640 medium supplemented with 2% FAF BSA, omitting Wnt3a from all samples. In some test samples using GDF-8, Wnt3a was replaced with a given concentration of small molecule compound, added only on the first day of definitive endoderm differentiation. These small molecules included: Compound 181 (1.25 μM in assay), Compound 180 (2.5 μM in assay), Compound 19 (10 μM in assay), Compound 202 (2.5 μM in assay), Compound 40 (5 μM in assay), Compound 34 (2.5 μM in assay), Compound 206 (2.5 μM in assay), and a commercially available GSK3 inhibitor IX BIO (10 μM in assay) (EMD Chemicals, Inc.; Cat #361550). At the conclusion of the first step of differentiation, cells from some wells were harvested for flow cytometry analysis to evaluate levels of CXCR4, a marker of definitive endoderm formation. Additional wells were harvested for RT-PCR analysis to measure other markers of differentiation.

At the conclusion of the first step of definitive endoderm differentiation, replicate sets of parallel wells from each treatment group were subjected to further step-wise differentiation. It is important to note that after the first differentiation step, all wells undergoing subsequent culture and differentiation received the same treatment. The protocol for this continuing differentiation is described below.

Step 2 of the differentiation protocol was carried out over two days. Cells were fed daily by aspirating the medium from each well and replacing with a fresh aliquot (0.5 ml) of DMEM:F12 medium (Invitrogen; Cat #11330-032) containing 2% FAF BSA, 50 ng/ml FGF7 (PeproTech; Cat #100-19), and 250 nM cyclopamine-KAAD (Calbiochem; Cat #239804).

Step 3 of the differentiation protocol was carried out over four days. Cells were fed daily by aspirating medium from each well and replacing with a fresh aliquot (0.5 ml) of DMEM-high glucose (Invitrogen; Cat #10569) supplemented with 0.1% Albumax (Invitrogen; Cat #: 11020-021), 0.5× Insulin-Transferrin-Selenium (ITS-X; Invitrogen; Cat #51500056), 50 ng/ml FGF7, 100 ng/ml Noggin (R&D Systems; Cat #3344-NG), 250 nM KAAD-cyclopamine, and 2 μM all-trans retinoic acid (RA) (Sigma-Aldrich; Cat #R2625). At the conclusion of the third step of differentiation, cells from some wells were harvested for analysis by RT-PCR to measure markers of differentiation.

Step 4 of the differentiation protocol was carried out over three days. Cells were fed daily by aspirating the medium from each well and replacing with a fresh aliquot (0.5 ml) of DMEM-high glucose supplemented with 0.1% Albumax, 0.5× Insulin-Transferrin-Selenium, 100 ng/ml Noggin, and 1 μM Alk 5 inhibitor (Axxora; Cat #ALX-270-445). At the conclusion of the fourth step of differentiation, cells from some wells were harvested for analysis by RT-PCR to measure markers of differentiation.

Step 5 of the differentiation protocol was carried out over seven days in DMEM-high glucose with 0.1% Albumax, 0.5× Insulin-Transferrin-Selenium, and 1 μM Alk 5 inhibitor. Medium in each well was aspirated and replaced with a fresh aliquot (0.5 ml) on all days. At the conclusion of the fifth step of differentiation, cells from some wells were harvested for analysis by RT-PCR to measure markers of differentiation. Other culture wells were subjected to high content image analysis for protein expression levels of insulin and glucagon.

FACS Analysis:

Cells for FACS analysis were blocked in a 1:5 solution of 0.5% human gamma-globulin (Sigma; Cat #G-4386) in PBS (Invitrogen; Cat #14040-133): BD FACS staining buffer—BSA (BD; Cat #554657) for 15 minutes at 4° C. Cells were then stained with antibodies for CD9 PE (BD; Cat #555372), CD99 PE (Caltag; Cat #MHCD9904) and CXCR4 APC (R&D Systems; Cat #FAB173A) for 30 minutes at 4° C. After a series of washes in BD FACS staining buffer, the cells were stained for viability with 7-AAD (BD; Cat #559925) and run on a BD FACSArray. A mouse IgG1K Isotype control antibody for both PE and APC was used to gate percent positive cells.

RT-PCR Analysis:

RNA samples were purified by binding to a silica-gel membrane (Rneasy Mini Kit, Qiagen, CA) in the presence of an ethanol-containing, high-salt buffer followed by washing to remove contaminants. The RNA was further purified using a TURBO DNA-free kit (Ambion, INC), and high-quality RNA was then eluted in water. Yield and purity were assessed by A260 and A280 readings on a spectrophotometer. CDNA copies were made from purified RNA using an ABI (ABI, CA) high capacity cDNA archive kit.

Unless otherwise stated, all reagents were purchased from Applied Biosystems. Real-time PCR reactions were performed using the ABI PRISM® 7900 Sequence Detection System. TAQMAN® UNIVERSAL PCR MASTER MIX® (ABI, CA) was used with 20 ng of reverse transcribed RNA in a total reaction volume of 20 al. Each cDNA sample was run in duplicate to correct for pipetting errors. Primers and FAM-labeled TAQMAN®probes were used at concentrations of 200 nM. The level of expression for each target gene was normalized using a human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) endogenous control previously developed by Applied Biosystems. Primer and probe sets are listed in Table 12. After an initial incubation at 50° C. for 2 min followed by 95° C. for 10 min, samples were cycled 40 times in two stages—a denaturation step at 95° C. for 15 sec followed by an annealing/extension step at 60° C. for 1 min. Data analysis was carried out using GENEAMP®7000 Sequence Detection System software. For each primer/probe set, a Ct value was determined as the cycle number at which the fluorescence intensity reached a specific value in the middle of the exponential region of amplification. Relative gene expression levels were calculated using the comparative Ct method. Briefly, for each cDNA sample, the endogenous control Ct value was subtracted from the gene of interest Ct to give the delta Ct value (ΔCt). The normalized amount of target was calculated as 2−ΔCt, assuming amplification to be 100% efficiency. Final data were expressed relative to a calibrator sample.

High Content Analysis:

At the conclusion of culture, assay plates were washed once with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for two hours at room temperature. After washing three times with PBS, Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Invitrogen; Cat #A21467) diluted 1:200 in PBS was added to each well. To counterstain nuclei, 5 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for fifteen minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging. Other primary antibodies used for analysis included 1:100 dilution mouse anti-human CDX2 (Invitrogen; Cat #397800), 1:100 dilution goat anti-human Pdx1 (Santa Cruz Biotechnology; Cat #SC-14664), 1:200 dilution rabbit anti-human insulin (Cell Signaling; Cat #C27C9), and 1:1500 dilution mouse anti-human glucagon (Sigma-Aldrich; Cat #G2654). Secondary antibodies used for analysis included 1:400 dilution Alexa Fluor 647 chicken anti-mouse IgG (Invitrogen; Cat #A-21463), 1:200 dilution Alexa Fluor 488 donkey anti-goat IgG (Invitrogen; Cat #A11055), 1:1000 dilution Alexa Fluor 647 chicken anti-rabbit IgG (Invitrogen; Cat #A21443), and 1:1000 dilution Alexa Fluor 488 chicken anti-mouse IgG (Invitrogen; Cat #A21200).

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Images were acquired from 25 fields per well. Measurements for total intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by the area of the cell. Background was eliminated based on acceptance criteria for gray-scale ranges between 200 and 4500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control.

Results: Results for representative differentiation markers are shown in FIG. 21 and Table 15 for cells harvested from each step of differentiation. In FIGS. 21A and B, flow cytometric results for CXCR4 are shown for various treatments during the first step of definitive endoderm differentiation. FIG. 21A shows the effects on CXCR4 expression from treatment with various compounds in combination with activin A. FIG. 21B shows the effects on CXCR4 from treatment with various compounds in combination with GDF-8. Compounds of the present invention in combination with activin A did not enhance CXCR4 expression. However, all of the compounds of the present invention tested in this Example enhanced CXCR4 expression in combination with GDF-8.

In FIGS. 21 C and 21D, normalized RT-PCR values for various differentiation markers at the end of step one of differentiation are shown for treatments applied during step one of the protocol, using selected compounds of the present invention in combination with activin A (FIG. 21C) or in combination with GDF-8 (FIG. 21D). Similar normalized RT-PCR values were evaluated at the conclusion of step three of the differentiation protocol (FIGS. 21E and 21F) and at the end of step four of the differentiation protocol (FIGS. 21G and 21H) and at the end of step 5 of the differentiation protocol (FIGS. 21I and 21J). Treatments during differentiation step 1, which combined a compound of the present invention with GDF-8, had improved expression of various endoderm and pancreatic markers relative to GDF-8 treatment alone (FIGS. 21 F and 21H and 21J). Treatments combining compounds of the present invention with activin A had minimal or no improvement in expression markers relative to treatment with activin A alone or activin A with Wnt3a (FIGS. 21E, and 21G and 21I). Table 15 summarizes comparative CT values for additional gene markers at the end of each differentiation step, comparing treatments during step one that combined activin A or GDF-8 with or without a compound of the present invention. At the conclusion of step five of differentiation, high content analysis was performed to measure cell numbers (FIGS. 21K and 21M) and protein expression of insulin and glucagon (FIGS. 21L and 21N). Treatment with GDF-8 during the first step of differentiation, alone or in combination with a compound of the present invention, resulted in insulin and glucagon expression at the conclusion of step five of differentiation, demonstrating that GDF-8 was able to substitute for activin A during the initiation of definitive endoderm formation and subsequently led to pancreatic hormonal cells. Collectively, these data show that addition of any of the respective small molecules had minimal effects on differentiation markers for treatments in combination with activin A. However, addition of a small molecule in combination with GDF-8 treatment had significant improved effects on immediate definitive endoderm differentiation at the conclusion of step 1 differentiation and also on downstream differentiation markers at the conclusion of steps 3, 4, and 5. Variability was observed within the panel of small molecules, perhaps attributable to the concentration of compound used in assay and/or mechanism of action.

Example 18 Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage that were Formed Using GDF-8 and a Compound of the Present Invention are Able to Release C-Peptide Following Transplantation into a Rodent

It was important to determine whether cells expressing markers characteristic of the pancreatic endoderm lineage generated in vitro by treatment with GDF-8 and a small molecule could produce functional endocrine cells in vivo. An in vivo transplant study was done to compare cells differentiated by treatment with activin A and Wnt3a versus treatment with GDF-8 and small molecule compounds.

Preparation of Cells:

Clusters of H1 human embryonic stem cells were grown on reduced growth factor MATRIGEL™ (Invitrogen; Cat #356231)-coated tissue culture plastic with passage on average every four days. MEF conditioned medium supplemented with 8 ng/ml bFGF was used for initial seeding and expansion. All human ES cell lines were maintained at passage numbers less than 50 and routinely evaluated for normal karyotype and absence of mycoplasma contamination.

Cell passage was performed by exposing cell cultures to a solution of 1 mg/ml dispase (Invitrogen; Cat #17105-041) for 5 to 7 minutes at 37° C. followed by rinsing the cell monolayer with MEF conditioned medium and gentle scraping to recover cell clusters. Cell clusters were centrifuged at low speed in MEF conditioned medium to remove residual dispase and then evenly resuspended in MEF conditioned medium supplemented with 8 ng/ml bFGF (PeproTech Inc.; Cat #100-18B) for seeding on reduced growth factor MATRIGEL (BD Biosciences; Cat #356231)-coated 6-well plates (Nunc; Cat #140685) at a 1:3 ratio using volumes of 2.5 ml/well. Daily feeding was conducted by aspirating spent culture medium from each well and replacing with an equal volume of fresh medium. Plates were maintained at 37° C., 5% CO₂ throughout the time in culture.

Cell Differentiation:

The differentiation process was started three days after the cells were seeded onto 6-well plates coated with reduced growth factor MATRIGEL™. A four-step protocol was used for the in vitro differentiation of H1 human embryonic stem cells to cells expressing markers characteristic of the pancreatic endoderm lineage. Step 1 was conducted over three days to generate definitive endoderm cells. On the first day of step 1, differentiation was initiated by aspirating spent culture medium and adding an equal volume of RPMI-1640 basal medium (Invitrogen; Cat #22400) with 2% Albumin Bovine Fraction V, Fatty Acid Free (FAF BSA) (Proliant Biologicals; Cat #SKU 68700) and 8 ng/ml bFGF. In one treatment group, cells were exposed to 100 ng/ml activin A (PeproTech; Cat #120-14) with 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN/CF). In a second treatment group, cells were exposed to 100 ng/ml GDF-8 (R&D Systems; Cat #788-G8) with 2.5 μM Compound 40. In a third treatment group, cells were exposed to 100 ng/ml GDF-8 (R&D Systems; Cat #788-G8) with 2.5 μM Compound 202. On the second and third day of step 1 of differentiation, cells in all treatment groups were fed with RPMI-1640 containing 2% FAF BSA, 8 ng/ml bFGF and either 100 ng/ml activin A (treatment group 1) or 100 ng/ml GDF-8 (treatment groups 2 and 3), without the addition of Wnt3a or a compound of the present invention. At the end of the third day of culture, one well from each treatment group was collected for FACS analysis.

Step 2 of the differentiation protocol was conducted over three days. Cells for all treatment groups were fed daily with DMEM:F12 (Invitrogen; Cat #11330-032) supplemented with 2% FAF BSA and 50 ng/ml FGF7 (PeproTech; Cat #100-19).

Step 3 of the differentiation protocol was conducted over four days. Cells for all treatment groups were fed daily with DMEM-high glucose (Invitrogen; Cat #10569) supplemented with 1% B27 (Invitrogen; Cat #: 17504-044), 50 ng/ml FGF7, 100 ng/ml Noggin (R&D Systems; Cat #3344-NG), 250 nM KAAD-cyclopamine (Calbiochem; Cat #239804), and 2 μM all-trans retinoic acid (RA) (Sigma-Aldrich; Cat #R2625).

Step 4 of the differentiation protocol was conducted over three days. Cells for all treatment groups were fed daily for the first two days with DMEM-high glucose supplemented with 1% B27, 100 ng/ml Noggin, and 1 μM ALK5 inhibitor (Axxora; Cat #ALX-270-445). On the third day, cells were lifted from the substratum by using a 20 μl tip (Rainin; Cat #RT-L10F) and a cell scraper (Corning; Cat #3008), then transferred to a 50 ml tube. The cells were allowed to sediment by gravity, and the supernatant was aspirated without disturbing the cell pellet. Cells were resuspended in DMEM-high glucose supplemented with 1% B27, 100 ng/ml Noggin and 1 μM ALK5 inhibitor, then cultured overnight in six-well Costar Ultra Low Attachment Microplates (Corning Inc., Cat #3471). On the following day, cells in suspension culture were collected and counted. Aliquots of 10×10⁶ cells/mouse were used for transplantation. Aliquots of 0.5×10⁶ cells were collected for RT-PCR analysis.

FIG. 22A shows flow cytometric results for definitive endoderm cells generated at the end of step 1 for each of the respective treatment groups. Treatment with activin A and Wnt3a or treatment with GDF-8 and a compound of the present invention resulted in cells expressing similar levels of CXCR4 (greater than 85%) at the end of step 1, suggesting that an equivalent definitive endoderm population of cells was derived from each treatment group.

Results for RT-PCR analysis for cells from each treatment group at the conclusion of step 4 of the differentiation protocol are shown in FIG. 22B. Cells differentiated to pancreatic endoderm (PE) using Activin A and Wnt3a or using GDF-8 and Compound 40 or using GDF-8 and Compound 202 expressed equivalent levels of PE markers: CDX2, MAFA, NGN3, NKX6.1, PDX1 and Ptf1 alpha. These results suggest that the differentiation protocol utilizing GDF-8 and a small molecule was equally effective in creating a pancreatic endoderm precursor population of cells.

Transplantation of Human Embryonic Stem Cells Treated According to the Methods of the Present Invention into Mice:

Five to six-week-old male scid-beige mice (C.B-Igh-1b/GbmsTac-Prkdc^(scid)-Lyst^(bg) N7) were purchased from Taconic Farms. Mice were housed in microisolator cages with free access to sterilized food and water. In preparation for surgery, mice were identified by ear tagging, their body weight was easured, and their blood glucose was determined using a hand held glucometer (LifeScan; One Touch). On the day of surgery, mice were anesthetized with a mixture of isolflurane and oxygen, and the surgical site was shaved with small animal clippers. Mice were dosed with 0.1 mg·kg Buprenex subcutaneously pre-operatively. The surgical site was prepared with successive washes of 70% isopropyl alcohol, 10% povidone-iodide, and 70% isopropyl alcohol, and a left lateral incision was made through the skin and muscle layers. The left kidney was externalized and kept moist with 0.9% sodium chloride. A 24G×¾″ I.V. catheter was used to penetrate the kidney capsule, and the needle was removed. The catheter was then advanced under the kidney capsule to the distal pole of the kidney. During preoperative preparation of the mice, cells for transplant were centrifuged in a 1.5 mL microfuge tube, and most of the supernatant was removed, leaving sufficient medium to collect the pellet of cells. The cells were collected into a Rainin Pos-D positive displacement pipette tip, and the pipette was inverted to allow the cells to settle by gravity. Excess medium was dispensed leaving a packed cell preparation for transplant. For transplantation, the Pos-D pipette tip was placed firmly in the hub of the catheter, and the cells were dispensed from the pipette through the catheter under the kidney capsule for delivery to the distal pole of the kidney. The lumen of the catheter was flushed with a small volume of culture medium to deliver any remaining cells, and the catheter was withdrawn. The kidney capsule was sealed with a low temperature cautery, and the kidney was returned to its original anatomical position. The muscle was closed with continuous sutures using 5-0 VICRYL sutures, and the skin was closed with wound clips. The mouse was removed from anesthesia and allowed to fully recover. Mice were dosed with 1.0 mg·kg Metacam subcutaneously post-operatively.

Following transplantation, mice were weighed once per week and blood glucose was measured twice per week. At various intervals following transplantation, mice were dosed with 3 g/kg glucose IP, and blood was drawn 60 minutes following glucose injection via the retro-orbital sinus into microfuge tubes containing a small amount of heparin. The blood was centrifuged, and the plasma was placed into a second microfuge tube, frozen on dry ice, for storage at −80° C. until the human C-peptide assay was performed. Human C-peptide levels were determined using the Mercodia/ALPCO Diagnotics Ultrasensitive C-peptide ELISA according to the manufacturer's instructions.

ELISA results for human C-peptide are shown in FIG. 23A to FIG. 23C for mice transplanted with cells from each of the respective treatment groups. No circulating human C-peptide was detected at four weeks post-transplant for any mice receiving cells from any of the treatment groups. At 8-weeks post-transplant, detectable C-peptide was found in one of two mice receiving cells treated with activin A and Wnt3a; one of three mice receiving cells treated with GDF-8 and Compound 40; and two of three mice receiving cells treated with GDF-8 and Compound 202. These results suggest that an equivalent endocrine precursor cell population could be derived from the differentiation protocol with GDF-8 and a small molecule and that the cells further matured in vivo to a glucose responsive, insulin secreting cell.

Example 19 Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage that were Formed Using GDF-8 are Able to Release C-Peptide Following Transplantation into a Rodent

It was important to demonstrate that cells differentiated with GDF-8 in the absence of activin A could also be further differentiated to an endocrine cell population capable of secreting human C-peptide in an in vivo rodent transplant model.

Preparation of Cells:

Clusters of H1 human embryonic stem cells were grown on reduced growth factor MATRIGEL™ (Invitrogen; Cat #356231)-coated tissue culture plastic with passage on average every four days. MEF conditioned medium supplemented with 8 ng/ml bFGF was used for initial seeding and expansion. All human ES cell lines were maintained at passage numbers less than 50 and routinely evaluated for normal karyotype and absence of mycoplasma contamination.

Cell passage was performed by exposing cell cultures to a solution of 1 mg/ml dispase (Invitrogen; Cat #17105-041) for 5 to 7 minutes at 37° C. followed by rinsing the cell monolayer with MEF conditioned medium and gentle scraping to recover cell clusters. Cell clusters were centrifuged at low speed in MEF conditioned medium to remove residual dispase and then evenly resuspended in MEF conditioned medium supplemented with 8 ng/ml bFGF (PeproTech Inc.; Cat #100-18B) for seeding on reduced growth factor MATRIGEL™ (BD Biosciences; Cat #356231)-coated 6-well plates (Nunc; Cat #140685) at a 1:3 ratio using volumes of 2.5 ml/well. Daily feeding was conducted by aspirating spent culture medium from each well and replacing with an equal volume of fresh medium. Plates were maintained at 37° C., 5% CO₂ throughout culture.

Cell Differentiation:

The differentiation process was started three days after the cells were seeded into 6-well plates. A four-step protocol was used for the in vitro differentiation of H1 human embryonic stem cells to cells expressing markers characteristic of the pancreatic endoderm lineage. Step 1 was conducted over three days to generate cells expressing markers characteristic of the definitive endoderm lineage. On the first day of step 1, differentiation was initiated by aspirating spent culture medium and adding an equal volume of RPMI-1640 basal medium (Invitrogen; Cat #22400) with 2% Albumin Bovine Fraction V, Fatty Acid Free (FAF BSA) (Proliant Biologicals; Cat #SKU 68700) and 8 ng/ml bFGF. In one treatment group, duplicate sets of cells were treated with 100 ng/ml GDF-8 (R&D Systems; Cat #788-G8) and 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN/CF). In a second treatment group, duplicate sets of cells were treated with 100 ng/ml GDF-8 and 2.5 μM Compound 40. On the second and third day of step 1 differentiation, cells in all treatment groups were fed with RPMI-1640 containing 2% FAF BSA, 8 ng/ml bFGF and 100 ng/ml GDF-8 but without the addition of Wnt3a or Compound 40. At the end of the third day of culture, one well from each treatment group was collected for FACS analysis.

Step 2 of the differentiation protocol was carried out over three days. Cells for all treatment groups were fed daily with DMEM:F12 (Invitrogen; Cat #11330-032) supplemented with 2% FAF BSA and 50 ng/ml FGF7 (PeproTech; Cat #100-19).

Step 3 of the differentiation protocol was carried out over four days. Cells for all treatment groups were fed daily with DMEM-high glucose (Invitrogen; Cat #10569) supplemented with 1% B27 (Invitrogen; Cat #: 17504-044), 50 ng/ml FGF7, 100 ng/ml Noggin (R&D Systems; Cat #3344-NG), 250 nM KAAD-cyclopamine (Calbiochem; Cat #239804), and 2 μM all-trans retinoic acid (RA) (Sigma-Aldrich; Cat #R2625).

Step 4 of the differentiation protocol was carried out over three days. Cells for all treatment groups were fed daily with DMEM-high glucose supplemented with 1% B27, 100 ng/ml Noggin and 1 μM ALK5 inhibitor (Axxora; Cat #ALX-270-445), and 100 ng/ml GDF-8 (R&D Systems; Cat #788-G8) during the first two days. On the third day of step 4, cells were harvested from the 6-well plates using a 20 μl tip (Rainin; Cat #RT-L10F) and a cell scraper (Corning; Cat #3008) and transferred to a 50 ml tube. Cells were allowed to sediment by gravity, and the supernatant was aspirated without disturbing the cell pellet. Cells were resuspended in DMEM-high glucose supplemented with 1% B27, 100 ng/ml Noggin, and 1 μM ALK5 inhibitor, then cultured overnight in six-well Costar Ultra Low Attachment Microplates (Corning Inc., Cat #3471). On the following day, cells in suspension culture were collected and counted. Aliquots of 10×10⁶ cells/mouse were used for transplantation. Aliquots of 0.5×10⁶ cells were collected for RT-PCR analysis.

FIG. 24A shows flow cytometric results for definitive endoderm cells generated at the end of step 1 for each of the respective treatment groups. Results for treatment with GDF-8 and Wnt3a or treatment with GDF-8 and Compound 40 expressed similar levels of CXCR4 at the end of step 1, suggesting that an equivalent and robust definitive endoderm population of cells resulted from each treatment group. Duplicate treatment sets were in strong agreement. Results prior to transplant for RT-PCR analysis at the conclusion of step 4 of the differentiation protocol are shown in FIG. 24B. Cells differentiated to pancreatic endoderm (PE) using GDF-8 and Wnt3a or GDF-8 and Compound 40 expressed equivalent levels of markers characteristic of the pancreatic endoderm lineage, such as: CDX2, MafA, Ngn3, NKX6.1, Pdx-1 and Ptf1A. These results demonstrate that the differentiation protocol utilizing GDF-8 and Wnt3a or GDF-8 and a compound of the present invention was effective in creating a pancreatic endoderm precursor population of cells. The differentiation protocol was conducted in two independent but identical treatment sets. Results from duplicate treatment sets were in strong agreement as shown by RT-PCR analysis.

Human Embryonic Stem Cell Transplantation into Mice:

Five to six-week-old male scid-beige mice (C.B-Igh-1b/GbmsTac-Prkdc^(scid)-Lyst^(bg) N7) were purchased from Taconic Farms. Mice were housed in microisolator cages with free access to sterilized food and water. In preparation for surgery, mice were identified by ear tagging, their body weight was measured, and their blood glucose was determined using a hand held glucometer (LifeScan; One Touch). On the day of surgery, mice were anesthetized with a mixture of isolflurane and oxygen, and the surgical site was shaved with small animal clippers. Mice were dosed with 0.1 mg·kg Buprenex subcutaneously pre-operatively. The surgical site was prepared with successive washes of 70% isopropyl alcohol, 10% povidone-iodide, and 70% isopropyl alcohol, and a left lateral incision was made through the skin and muscle layers. The left kidney was externalized and kept moist with 0.9% sodium chloride. A 24G×34″ I.V. catheter was used to penetrate the kidney capsule, and the needle was removed. The catheter was then advanced under the kidney capsule to the distal pole of the kidney. During preoperative preparation of the mice, cells for transplant were centrifuged in a 1.5 mL microfuge tube, and most of the supernatant was removed, leaving sufficient medium to collect the pellet of cells. The cells were collected into a Rainin Pos-D positive displacement pipette tip, and the pipette was inverted to allow the cells to settle by gravity. Excess medium was dispensed leaving a packed cell preparation for transplant. For transplantation, the Pos-D pipette tip was placed firmly in the hub of the catheter, and the cells were dispensed from the pipette through the catheter under the kidney capsule for delivery to the distal pole of the kidney. The lumen of the catheter was flushed with a small volume of culture medium to deliver any remaining cells, and the catheter was withdrawn. The kidney capsule was sealed with a low temperature cautery, and the kidney was returned to its original anatomical position. The muscle was closed with continuous sutures using 5-0 vicryl, and the skin was closed with wound clips. The mouse was removed from anesthesia and allowed to fully recover. Mice were dosed with 1.0 mg·kg Metacam subcutaneously post-operatively.

Following transplantation, mice were weighed once per week and blood glucose was measured twice per week. At various intervals following transplantation, mice were dosed with 3 g/kg glucose IP, and blood was drawn 60 minutes following glucose injection via the retro-orbital sinus into microfuge tubes containing a small amount of heparin. The blood was centrifuged, and the plasma was placed into a second microfuge tube, frozen on dry ice, for storage at −80° C. until the human C-peptide assay was performed. Human C-peptide levels were determined using the Mercodia/ALPCO Diagnostics Ultrasensitive C-peptide ELISA according to the manufacturer's instructions. ELISA results for human C-peptide are shown in FIG. 24C and FIG. 24D for mice transplanted with cells from each of the respective treatment groups. Similar levels of human C-peptide were detectable at 8 weeks post-transplant for each treatment category, indicating that an equivalent endocrine precursor cell population could be derived from the differentiation protocol using GDF-8 and Wnt3a or GDF-8 and a compound of the present invention.

Example 20 Evaluation of the Potential of Inhibitors of CDK, GSK3, and TRK to Differentiate Human Embryonic Stem Cells into Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage

A subset of 14 proprietary small molecules, known to have specificity for the CDK, GSK3, and/or TRK signaling pathways were evaluated for their potential to differentiate human embryonic stem cells to cells expressing markers characteristic of the definitive endoderm lineage.

Cell Assay Seeding:

Briefly, clusters of H1 human embryonic stem cells were grown on reduced growth factor Matrigel™ (Invitrogen; Cat #356231) coated tissue culture plastic. Cells were passaged using collagenase (Invitrogen; Cat #17104-019) treatment and gentle scraping, washed to remove residual enzyme, and plated with even dispersal at a ratio of 1:1 (surface area) on reduced growth factor MATRIGEL™ (BD Biosciences; Cat #356231)-coated 96-well black plates (Packard ViewPlates; PerkinElmer; Cat #6005182) using volumes of 100 μl/well. Cells were allowed to attach and then recover log phase growth over a 1 to 3 day time period, feeding daily with MEF conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB). Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of assay.

Preparation of Compounds and Assay:

Screening was conducted using the compounds described in Table 16. In addition Compound 34 was included as a positive control, as demonstrated in previous examples. Compounds were made available as 5 mM stocks in 96-well plate format, solubilized in 100% DMSO (Sigma; Cat #D2650) and stored at −80° C. The library compounds were further diluted to an intermediate concentration of 0.2 mM in 50 mM HEPES (Invitrogen; Cat #15630-080), 20% DMSO and stored at 4° C. Test conditions were performed in triplicate, feeding on alternating days over a four-day assay period. Assay was initiated by aspirating culture medium from each well followed by three washes in PBS (Invitrogen; Cat #14190) to remove residual growth factors. On the first day of assay, test volumes of 200 μl per well were added to each well using DMEM:F12 base medium (Invitrogen; Cat #11330-032) supplemented with 0.5% FCS (HyClone; Cat #SH30070.03) and 100 ng/ml GDF-8 (R&D Systems, Cat #788-G8) plus 2.5 μM compound. A parallel set of test samples were treated in an identical manner but omitting GDF-8 from the medium. On the third day of assay, test volumes of 100 μl per well were added to each well using DMEM:F12 base medium supplemented with 2% FCS plus 100 ng/ml GDF-8 (R&D Systems, Cat #788-G8). GDF-8 was omitted from test samples that did not get treated with GDF-8 on the first day of assay. Positive control samples contained the same base medium supplemented with FCS and 100 ng/ml recombinant human activin A (PeproTech; Cat #120-14) throughout the four day assay along with Wnt3a (20 ng/ml) addition on days 1 and 2. Negative control samples contained DMEM:F12 base medium supplemented with FCS.

High Content Analysis:

At the conclusion of four-days of culture, assay plates were washed twice with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for one hour at room temperature. Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Molecular Probes; Cat #AZ1467) was diluted 1:200 in PBS and added to each sample well after washing three times with PBS. To counterstain nuclei, 4 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for ten minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Exposure times were optimized from positive control wells and from untreated negative control wells stained with secondary antibody alone. Images from 15 fields per well were acquired to compensate for any cell loss during the bioassay and subsequent staining procedures. Measurements for total cell number and total SOX17 intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell multiplied by area of the cell. Background was eliminated based on acceptance criteria of gray-scale ranges between 200 and 3500. Average data from triplicate wells were collected. The percentage of treated wells relative to the positive control was calculated.

Results for this screen are shown in Table 17. None of the small molecules induced significant SOX17 expression in the absence of GDF-8 during the four day differentiation process. Compound 34 served as an experimental control and induced significant SOX17 expression in the presence of GDF-8, equivalent to levels observed with the positive control using activin A and Wnt3a. The remaining compounds of the present invention tested in this example showed a range of activities with weak to moderate induction of SOX17 expression. Of note, differentiation activity in this subset of compounds was observed in association with selectivity for all three enzymatic signal pathways, making it difficult to conclusively determine a clear mechanism of action.

Example 21 Screening for Analogues of the Compounds of the Present Invention that are Capable of Mediating the Formation of Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage

Based on the structures for the compounds of the present invention, an analog search was conducted and 118 analogues were found. Initial screening determined that some analogues were able to induce definitive endoderm differentiation in the absence of activin A in combination with other growth factors. It was important to determine if these analogues could also induce definitive endoderm differentiation in combination with only GDF-8.

Cell Assay Seeding:

Briefly, clusters of H1 human embryonic stem cells were grown on reduced growth factor Matrigel™ (Invitrogen; Cat #356231)-coated tissue culture plastic. Cells were passaged using collagenase (Invitrogen; Cat #17104-019) treatment and gentle scraping, washed to remove residual enzyme, and plated with even dispersal at a ratio of 1:1 (surface area) on reduced growth factor MATRIGEL™ (BD Biosciences; Cat #356231)-coated 96-well black plates (Packard ViewPlates; PerkinElmer; Cat #6005182) using volumes of 100 μl/well. Cells were allowed to attach and then recover log phase growth over a 1 to 3 day time period, feeding daily with MEF conditioned medium supplemented with 8 ng/ml bFGF (R&D Systems; Cat #233-FB). Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of assay.

Preparation of Compounds and Assay:

Screening was conducted using a library of the analogue compounds. Compounds from this library were made available as 5 mM stocks in 96-well plate format, solubilized in 100% DMSO (Sigma; Cat #D2650) and stored at −80° C. The library compounds were further diluted to an intermediate concentration of 0.2 mM in 50 mM HEPES (Invitrogen; Cat #15630-080), 20% DMSO and stored at 4° C. Test conditions were performed in triplicate, feeding on alternating days over a four-day assay period. Assays were initiated by aspirating culture medium from each well followed by three washes in PBS (Invitrogen; Cat #14190) to remove residual growth factors. On the first day of assay, test volumes of 200 μl per well were added to each well using DMEM:F12 base medium (Invitrogen; Cat #11330-032) supplemented with 0.5% FCS (HyClone; Cat #SH30070.03) and 200 ng/ml GDF-8 (R&D Systems, Cat #788-G8) plus 2.5 μM compound. On the third day of assay, test volumes of 100 μl per well were added to each well using DMEM:F12 base medium supplemented with 2% FCS plus 200 ng/ml GDF-8 (R&D Systems, Cat #788-G8). Positive control samples contained the same base medium supplemented with FCS and 100 ng/ml recombinant human activin A (PeproTech; Cat #120-14) throughout the four-day assay along with Wnt3a (20 ng/ml) on days 1 and 2. Negative control samples contained DMEM:F12 base medium supplemented with FCS, adding Wnt3a on days 1 and 2 but omitting treatment with activin A.

High Content Analysis:

At the conclusion of four-days of culture, assay plates were washed twice with PBS (Invitrogen; Cat #14190), fixed with 4% paraformaldehyde (Alexis Biochemical; Cat #ALX-350-011) at room temperature for 20 minutes, then washed three times with PBS and permeabilized with 0.5% Triton X-100 (Sigma; Cat #T8760-2) for 20 minutes at room temperature. Cells were washed again three times with PBS and blocked with 4% chicken serum (Invitrogen; Cat #16110082) in PBS for 30 minutes at room temperature. Primary antibody (goat anti-human SOX17; R&D Systems; Cat #AF1924) was diluted 1:100 in 4% chicken serum and added to each well for one hour at room temperature. Alexa Fluor 488 conjugated secondary antibody (chicken anti-goat IgG; Molecular Probes; Cat #AZ1467) was diluted 1:200 in PBS and added to each sample well after washing three times with PBS. To counterstain nuclei, 4 μg/ml Hoechst 33342 (Invitrogen; Cat #H3570) was added for ten minutes at room temperature. Plates were washed once with PBS and left in 100 μl/well PBS for imaging.

Imaging was performed using an IN Cell Analyzer 1000 (GE Healthcare) utilizing the 51008bs dichroic for cells stained with Hoechst 33342 and Alexa Fluor 488. Exposure times were optimized from positive control wells and from untreated negative control wells stained with secondary antibody alone. Images from 15 fields per well were acquired to compensate for any cell loss during the bioassay and subsequent staining procedures. Measurements for total cell number and total SOX17 intensity were obtained from each well using IN Cell Developer Toolbox 1.7 (GE Healthcare) software. Segmentation for the nuclei was determined based on gray-scale levels (baseline range 100-300) and nuclear size. Averages and standard deviations were calculated for each replicate data set. Total SOX17 protein expression was reported as total intensity or integrated intensity, defined as total fluorescence of the cell times area of the cell. Background was eliminated based on acceptance criteria of gray-scale ranges between 200 to 3500. Total intensity data were normalized by dividing total intensities for each well by the average total intensity for the positive control. Normalized data were calculated for averages and standard deviations for each replicate set.

Screening results are shown in Table 18 from four assay plates in this single experiment. Compounds are ranked with respect to SOX17 expression as a percentage of the positive control treatment with activin A and Wnt3a. This assay identified a list of 12 new analogue hits as shown in Table 19.

Example 22 Human Embryonic Stem Cells Grown on Microcarriers can be Differentiated into Cells Expressing Markers Characteristic of the Definitive Endoderm Lineage According to the Methods of the Present Invention

For purposes of differentiation and production of large numbers of endocrine cells under scalable conditions, it was important to show that human embryonic stem cells could be grown and differentiated to definitive endoderm on microcarrier beads using the methods of the present invention.

Preparation of Cells for Assay and Differentiation:

H1 p49Cβ cells were routinely grown on Cytodex3 beads (GE Healthcare Life Sciences, NJ) in a 125 ml spinner flask, according to the methods described in U.S. Patent Application No. 61/116,447. After seven days, cells and beads were transferred to a 6 well plate at a ratio of 30 cm² bead surface area per well, and the plate was placed on a rocking platform. Cells on beads in the positive control treatment well (designated AA/Wnt3a) were differentiated with addition of 100 ng/ml activin A (PeproTech; Cat #120-14) and 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN/CF) for two days followed by 100 ng/ml activin A and 8 ng/ml bFGF (PeproTech Inc.; Cat #: 100-18B) for one day in RPMI-1640 (Invitrogen; Cat #: 22400) with 2% Fatty Acid Free BSA (MP Biomedicals, Inc; Cat #152401) using volumes of 2 ml/well. Compound 34, at a final concentration of 2.5 μM was added to a negative control treatment well (designated CMP alone (JNJ alone)) in RPMI-1640 with 2% Fatty Acid Free BSA (2 ml/well) for three days in the absence of any other growth factor treatment. A third treatment well (designated CMP+8) received Compound 34 at 2.5 μM plus 50 ng/ml GDF-8 (R&D Systems, Cat #788-G8) in RPMI-1640 with 2% Fatty Acid Free BSA (2 ml/well) for three days. A fourth treatment well (designated CMP+8+D) received Compound 34 at 2.5 μM with 50 ng/ml GDF-8 and 50 ng/ml PDGF-D in RPMI-1640 with 2% Fatty Acid Free BSA (2 ml/well) for three days. A fifth treatment well (designated CMP+8+D+V (JNJ+8+D+V)) received Compound 34 at 2.5 μM with 50 ng/ml GDF-8, 50 ng/ml PDGF-D, and 50 ng/ml VEGF in RPMI-1640 with 2% Fatty Acid Free BSA (2 ml/well) for three days. A sixth treatment well (designated CMP+8+D+V+M (JNJ+8+D+V+M)) received Compound 34 at 2.5 μM with 50 ng/ml GDF-8, 50 ng/ml PDGF-D, 50 ng/ml VEGF, and 20 ng/ml Muscimol in RPMI-1640 with 2% Fatty Acid Free BSA (2 ml/well) for three days. All media and treatments were exchanged daily.

At the conclusion of treatment and culture, cells were harvested from the beads, according to the methods described in U.S. Patent Application No. 61/116,447. The harvested cells were counted and analyzed by flow cytometry, according to the methods described above.

Results are shown in FIG. 25. As shown in FIG. 25A, similar numbers of cells were recovered for all treatment groups undergoing differentiation. As shown in FIG. 25B, cells treated with the Compound 34 (JNJ) alone did not differentiate into CXCR4 positive cells. The positive control treatment, adding activin A and Wnt3a during differentiation, induced expression of CXCR4 in 68% of the resulting cell population. Compound 34 added with the various growth factor combinations induced CXCR4 expression in 50% of the cells, on average. Of note, equivalent levels of CXCR4 expression were observed during treatment with Compound 34 in combination with a single growth factor, GDF-8, or in combination with multiple growth factors that included GDF-8. This proves that Compound 34 in combination with at least GDF-8 can substitute for activin A and Wnt3a to promote definitive endoderm differentiation. This example also shows that the treatment procedure is effective for cells grown and differentiated on microcarrier beads.

Example 23 The Compounds of the Present Invention, Together with GDF-8 Enhance Cell Proliferation

A previous example showed that GDF-8 is able to replace activin A to differentiate human embryonic stem cells to cells expressing markers characteristic of the definitive endoderm lineage. It was important to know the relative potencies of GDF-8 and activin A with respect to definitive endoderm formation. A dose response assay was conducted using equivalent concentrations of each growth factor to compare results during human embryonic stem cell differentiation.

The compounds of the present invention used in combination with GDF-8 during definitive endoderm differentiation were evaluated for their ability to induce cell proliferation. Results were compared to treatment with activin A or GDF-8 alone.

Preparation of Cells for Assay:

Stock cultures of human embryonic stem cells (H1 human embryonic stem cell line) were maintained in an undifferentiated, pluripotent state on reduced growth factor MATRIGEL™ (BD Biosciences; Cat #356231)-coated dishes in MEF conditioned medium with passage on average every four days. Passage was performed by exposing cell cultures to a solution of 1 mg/ml dispase (Invitrogen, Cat #: 17105-041) for 5 to 7 minutes at 37° C. followed by rinsing the monolayer with MEF conditioned culture medium and gentle scraping to recover cell clusters. Clusters were centrifuged at low speed to collect a cell pellet and remove residual dispase. Cell clusters were split at a 1:3 or 1:4 ratio for routine maintenance culture or a 1:1 ratio for immediate assay. All human embryonic stem cell lines were maintained at passage numbers less than 50 and routinely evaluated for normal karyotypic phenotype and for absence of mycoplasma contamination.

Cell clusters used in the assay were evenly resuspended in MEF conditioned medium supplemented with 8 ng/ml bFGF and seeded onto reduced growth factor MATRIGEL™-coated 96-well Packard VIEWPLATES (PerkinElmer; Cat #6005182) in volumes of 100 μl/well. MEF conditioned medium supplemented with 8 ng/ml bFGF was used for initial seeding and expansion. Daily feeding was conducted by aspirating spent culture medium from each well and replacing with an equal volume of fresh medium. A background set of wells in each assay plate was not seeded with cells but was treated throughout assay with basal media conditions. Plates were maintained at 37° C., 5% CO₂ in a humidified box throughout the duration of assay.

Assay:

The assay was initiated by aspirating the culture medium from each well and adding back a final aliquot (100 μl) of test medium. Test conditions were performed in triplicate over a total three-day assay period, feeding daily by aspirating and replacing the medium from each well with fresh test medium. Identical assays were set up simultaneously in parallel for evaluation at the end of 24, 48, and 72 hours.

On the first day of assay, all wells containing cells received an aliquot (80 μl) of RPMI-1640 medium (Invitrogen; Cat #: 22400) supplemented with 2.5% Albumin Bovine Fraction V, Fatty Acid Free (FAF BSA; 2% in final assay) (Proliant Inc. Cat #: SKU 68700). Various control and test samples were created at 5× concentration to be added to appropriate wells (20 μl per well). Control conditions included the following, with final growth factor concentrations as indicated: 1) basal medium with 2% FAF BSA; 2) 100 ng/ml activin A (PeproTech; Cat #120-14) with 8 ng/ml bFGF (PeproTech; Cat #100-18B); 3) 100 ng/ml activin A with 8 ng/ml bFGF and 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN/CF); 4) 100 ng/ml GDF-8 (R&D Systems, Cat #788-G8) with 8 ng/ml bFGF; 5) GDF-8 with 8 ng/ml bFGF and 20 ng/ml Wnt3a. Cells in an additional set of control wells were treated with MEF conditioned medium throughout the assay. In some control samples using GDF-8, Wnt3a was replaced with a compound of the present invention. For experimental test samples, eight different compounds were diluted two-fold in series to create three different dose concentrations then combined with 100 ng/ml GDF-8 and 8 ng/ml bFGF. These small molecules included proprietary compounds Compound 181, Compound 180, Compound 19, Compound 202, Compound 40, Compound 34, Compound 56, and a commercially available GSK3 inhibitor BIO (EMD Chemicals, Inc.; Cat #361550). On the second and third day of assay, all wells for control and experimental samples were aspirated and fed again using identical treatment conditions except that Wnt3a was removed from some control wells.

MTS Assay:

At the conclusion of 24, 48, or 72 hours of culture, one set of assay plates was subjected to a MTS assay (Promega; Cat #G3581), following the manufacturer's instructions. In brief, 20 μl of MTS was added to each well, and assay plates were incubated at 37° C., 5% CO₂ for four hours prior to taking OD490 readings. Statistical measures were calculated minus background (i.e. treatment wells without cells) to determine mean values for each triplicate set in addition to a standard error of the mean.

The MTS assay is a measure of cellular metabolic activity in the enzymatic reduction of a tetrazolium compound to a formazan product. At a single time point, the MTS assay can be used as a comparative indicator of cell viability. MTS assays evaluated in parallel at sequential time points can add additional information regarding increases in cellular metabolic activity which in turn can be correlated with cell proliferation for each treatment condition. FIG. 26A shows OD490 readings for all control treatments over the three day assay period. Cells treated with conditioned medium showed little change in OD490 over three days, indicating that cell numbers in this treatment group remained static. In contrast, cells cultured in basal medium without growth factors (no treatment), showed a steady decline in OD490 correlated with a loss in cell number over time. Activin A treatments during the differentiation process, with and without Wnt3a, showed incremental increases in OD490, indicating significant expansion of the cell population over time. GDF-8 treatment in the absence of Wnt3a resulted in a decrease in OD490 relative to activin A treatment; this was noticeable on the first day and sustained throughout all three days of culture. Addition of Wnt3a to the GDF-8 treatment group resulted in a recovery and increase in OD490 by the third day of culture.

FIG. 26B through FIG. 26I show MTS assay results for treatment with a small molecule inhibitor in combination with GDF-8. OD490 readings from treatments with a compound of the present invention and GDF-8 were equivalent to or exceeded results from treatment with activin A. In all cases, an optimal concentration of each small molecule combined with GDF-8 resulted in improved OD490 readings over the three day assay relative to treatment with GDF-8 alone. This suggests that the compounds of the present invention are important for inducing proliferation and expansion of a cell population during definitive endoderm differentiation.

Example 24 Human Embryonic Stem Cells Grown on Microcarriers can be Differentiated into Endocrine Progenitor Cells According to the Methods of the Present Invention

For purposes of differentiation and production of large numbers of endocrine cells under industrial conditions, it was important to show that human embryonic stem cells could be grown and differentiated to endocrine progenitor cells on microcarrier beads using a protocol without activin A.

Preparation of Cells for Assay and Differentiation:

H1 p45 cells were grown on Cytodex3 beads (GE Healthcare; Cat #17-0485-01) in a 6 well ultra low attachment plate (Costar; Cat #3471) placed on a rocking platform at about 1 rotation every 10 seconds (Vari Mix, Thermo Scientific, Cat #M79735). MEF conditioned media was changed daily for six days. Then the media was changed to the following treatments to initiate endoderm differentiation. Cells on beads in the positive control treatment well (designated AA+Wnt) were differentiated with addition of 100 ng/ml activin A (PeproTech; Cat #120-14), 8 ng/ml bFGF (PeproTech Inc.; Cat #: 100-18B), and 20 ng/ml Wnt3a (R&D Systems; Cat #1324-WN/CF) for one day followed by 100 ng/ml activin A and 8 ng/ml bFGF (PeproTech Inc.; Cat #: 100-18B) for two days in RPMI-1640 (Invitrogen; Cat #: 22400) with 2% Fatty Acid Free BSA (Proliant Biomedicals, Inc; SKU #68700) using volumes of 2 ml/well. A second treatment well (designated GDF-8+MCX) received Compound 202 at 2.5 μM plus 200 ng/ml GDF-8 (R&D Systems, Cat #788-G8) and 8 ng/ml bFGF for one day followed by two days with 200 ng/ml GDF-8 and 8 ng/ml bFGF in RPMI-1640 with 2% Fatty Acid Free BSA (2 ml/well) media. A third treatment well (designated GDF-8+Wnt) received 200 ng/ml GDF-8 with 20 ng/ml Wnt3a and 8 ng/ml bFGF for one day followed by two days with 200 ng/ml GDF-8 and 8 ng/ml bFGF in RPMI-1640 with 2% Fatty Acid Free BSA (2 ml/well) media. All media and treatments were exchanged daily.

At the conclusion of treatment and culture, cells were harvested and counted to determine cell recovery and undergo flow cytometric analysis. High levels of CXCR4 and CD99 was seen following all three treatment regiments (FIG. 27A). Cell number varied between samples (FIG. 27B). A lower cell number was observed in samples treated with GDF-8 and at the definitive endoderm and fourth stage than the other treatment groups. This suggests that the compounds of the present invention may increase proliferation of the cells during differentiation.

At the end of stage 3 the endodermal genes PDX1, HNF4 alpha, and CDX2 are expressed in the cells (FIG. 27C, D). Treatment of the cells with GDF-8 and a compound of the present invention during stage one of differentiation resulted in better expression of Pdx1 than the control differentiation treatment. At the end of stage 4, endodermal genes were up regulated further (FIG. 27E, F). These results conclude that GDF-8 plus Compound 202 can replace activin A and Wnt3a for definitive endoderm differentiation resulting in pancreatic endoderm formation.

Publications cited throughout this document are hereby incorporated by reference in their entirety. Although the various aspects of the invention have been illustrated above by reference to examples and preferred embodiments, it will be appreciated that the scope of the invention is defined not by the foregoing description but by the following claims properly construed under the principles of patent law.

TABLE 1 Cell Number Sox17 Expression % of % of Avg. total positive Avg. Total positive Plate # Compound # Cell Number control Intensity control plate 5 no Activin A (with Wnt3a) 7159 67.42 8.12E+06 2.51 plate 5 Activin A/Wnt3a 10619 100.00 3.23E+08 100.00 plate 5 Compound 58 4848 45.66 −1.60E+06  −0.49 plate 5 Compound 59 20 0.19 −4.62E+06  −1.43 plate 5 Compound 60 3348 31.52 −2.33E+05  −0.07 plate 5 Compound 61 2931 27.60 −3.05E+06  −0.94 plate 5 Compound 62 7171 67.53 −2.04E+06  −0.63 plate 5 Compound 3 14211 133.82 −2.34E+06  −0.73 plate 6 no Activin A (with Wnt3a) 3264 32.97 2.52E+06 0.80 plate 6 Activin A/Wnt3a 9902 100.00 3.14E+08 100.00 plate 6 Compound 63 1917 19.36 4.75E+05 0.15 plate 6 Compound 26 5434 54.88 −6.33E+05  −0.20 plate 6 Compound 27 6288 63.50 −1.13E+06  −0.36 plate 6 Compound 28 4121 41.62 −1.89E+06  −0.60 plate 6 Compound 29 5164 52.15 −1.66E+06  −0.53 plate 6 Compound 30 4726 47.73 −1.23E+06  −0.39 plate 7 no Activin A (with Wnt3a) 9545 47.57 −4.87E+06  −0.99 plate 7 Activin A/Wnt3a 20064 100.00 4.92E+08 100.00 plate 7 Compound 31 7230 36.03 −3.45E+06  −0.70 plate 7 Compound 32 14655 73.04 −3.03E+06  −0.62 plate 7 Compound 33 13891 69.23 −8.11E+06  −1.65 plate 7 Compound 34 11674 58.18 −2.24E+06  −0.46 plate 7 Compound 35 15379 76.65 −7.30E+06  −1.48 plate 7 Compound 36 8356 41.65 −4.57E+06  −0.93 plate 8 no Activin A (with Wnt3a) 6868 36.97 −2.31E+06  −0.52 plate 8 Activin A/Wnt3a 18575 100.00 4.47E+08 100.00 plate 8 Compound 37 9048 48.71 −3.51E+06  −0.79 plate 8 Compound 38 11361 61.16 −4.31E+06  −0.96 plate 8 Compound 39 7054 37.98 −3.83E+06  −0.86 plate 8 Compound 40 8104 43.63 −4.59E+06  −1.03 plate 1 no Activin A (with Wnt3a) 2972 27.98 1.64E+07 19.74 plate 1 Activin A/Wnt3a 3126 29.44 8.33E+07 100.00 plate 1 Compound 64 2201 20.72 1.71E+07 20.52 plate 1 Compound 65 3030 28.53 2.83E+07 33.95 plate 1 Compound 66 1990 18.74 2.36E+07 28.30 plate 1 Compound 67 2074 19.53 2.63E+07 31.55 plate 1 Compound 68 1432 13.48 1.03E+07 12.39 plate 1 Compound 69 2593 24.42 2.62E+07 31.43 plate 1 Compound 70 2236 21.05 2.59E+07 31.11 plate 1 Compound 71 2996 28.22 3.07E+07 36.92 plate 1 Compound 72 2179 20.52 1.21E+07 14.50 plate 1 Compound 73 2817 26.53 2.93E+07 35.25 plate 1 Compound 74 2853 26.86 2.25E+07 27.01 plate 1 Compound 75 1689 15.91 1.42E+07 17.05 plate 1 Compound 76 2324 21.89 1.48E+07 17.81 plate 1 Compound 77 2306 21.71 2.04E+07 24.55 plate 1 Compound 78 3298 31.06 2.58E+07 31.00 plate 1 Compound 79 2855 26.88 2.79E+07 33.47 plate 1 Compound 80 3603 33.93 3.22E+07 38.62 plate 1 Compound 81 2263 21.31 1.07E+07 12.91 plate 1 Compound 82 1210 11.39 1.36E+07 16.33 plate 1 Compound 83 1805 17.00 1.82E+07 21.87 plate 1 Compound 84 2024 19.06 2.48E+07 29.80 plate 1 Compound 85 2840 26.74 3.45E+07 41.44 plate 1 Compound 86 1447 13.63 8.43E+06 10.13 plate 1 Compound 87 5336 50.25 4.20E+07 50.38 plate 2 no Activin A (with Wnt3a) 4033 35.50 2.14E+07 21.70 plate 2 Activin A/Wnt3a 4292 37.78 9.86E+07 100.00 plate 2 Compound 88 3416 30.06 4.17E+07 42.28 plate 2 Compound 89 4751 41.82 2.11E+07 21.40 plate 2 Compound 90 4542 39.98 3.03E+07 30.70 plate 2 Compound 91 1401 12.33 1.29E+06 1.31 plate 2 Compound 92 4210 37.06 2.95E+07 29.90 plate 2 Compound 93 4157 36.59 2.29E+07 23.26 plate 2 Compound 94 4046 35.61 2.85E+07 28.91 plate 2 Compound 95 8368 73.66 4.02E+07 40.72 plate 2 Compound 96 3695 32.53 2.92E+07 29.57 plate 2 Compound 97 3437 30.26 2.41E+07 24.44 plate 2 Compound 98 4178 36.77 3.75E+07 38.07 plate 2 Compound 99 3739 32.91 2.10E+07 21.29 plate 2 Compound 100 2275 20.02 1.27E+07 12.86 plate 2 Compound 101 3496 30.77 2.98E+07 30.17 plate 2 Compound 102 4874 42.90 2.10E+07 21.32 plate 2 Compound 103 4228 37.22 2.69E+07 27.32 plate 2 Compound 104 6115 53.82 4.93E+07 49.99 plate 2 Compound 105 6484 57.07 5.03E+07 50.95 plate 2 Compound 106 4211 37.06 3.94E+07 40.00 plate 2 Compound 107 2853 25.11 1.78E+07 18.04 plate 2 Compound 108 3779 33.27 2.39E+07 24.26 plate 2 Compound 108 2869 25.26 2.04E+07 20.71 plate 2 Compound 110 4398 38.71 2.53E+07 25.65 plate 3 no Activin A (with Wnt3a) 2589 91.17 1.17E+07 5.89 plate 3 Activin A/Wnt3a 6933 244.13 1.98E+08 100.00 plate 3 Compound 111 6816 240.04 5.33E+07 26.90 plate 3 Compound 112 5357 188.66 3.52E+07 17.74 plate 3 Compound 113 6002 211.37 8.55E+07 43.11 plate 3 Compound 114 3308 116.49 3.85E+07 19.44 plate 3 Compound 115 5007 176.31 3.96E+07 19.95 plate 3 Compound 116 3802 133.89 3.12E+07 15.75 plate 3 Compound 117 6521 229.64 4.16E+07 20.97 plate 3 Compound 118 6128 215.81 5.53E+07 27.91 plate 3 Compound 119 4184 147.35 3.41E+07 17.21 plate 3 Compound 120 2489 87.66 2.87E+07 14.49 plate 3 Compound 121 4985 175.54 3.94E+07 19.87 plate 3 Compound 25 4151 146.17 4.03E+07 20.32 plate 3 Compound 122 6407 225.61 4.15E+07 20.95 plate 3 Compound 123 4465 157.24 5.35E+07 26.99 plate 3 Compound 124 4417 155.53 4.67E+07 23.55 plate 3 Compound 125 6367 224.23 5.73E+07 28.93 plate 3 Compound 126 6157 216.82 7.47E+07 37.70 plate 3 Compound 127 5593 196.97 5.61E+07 28.28 plate 3 Compound 128 4160 146.50 4.91E+07 24.77 plate 3 Compound 129 3778 133.03 3.54E+07 17.88 plate 3 Compound 130 4357 153.43 4.15E+07 20.92 plate 3 Compound 131 6135 216.05 4.28E+07 21.61 plate 3 Compound 132 4421 155.69 4.58E+07 23.12 plate 3 Compound 133 7069 248.94 6.52E+07 32.88 plate 4 no Activin A (with Wnt3a) 3274 86.62 1.25E+07 12.79 plate 4 Activin A/Wnt3a 4158 110.03 9.79E+07 100.00 plate 4 Compound 134 5277 139.62 3.43E+07 35.04 plate 4 Compound 64 5657 149.67 3.38E+07 34.48 plate 4 Compound 135 2790 73.83 1.63E+07 16.63 plate 4 Compound 34 4774 126.33 4.35E+07 44.47 plate 4 Compound 136 4881 129.16 3.20E+07 32.73 plate 4 Compound 137 1740 46.05 9.16E+06 9.35 plate 4 Compound 30 6367 168.46 4.22E+07 43.13 plate 4 Compound 37 5377 142.27 2.85E+07 29.14 plate 4 Compound 138 7722 204.32 3.07E+07 31.37 plate 4 Compound 139 3574 94.56 1.30E+07 13.32 plate 4 Compound 140 3893 103.00 1.12E+07 11.46 plate 4 Compound 39 6114 161.77 3.45E+07 35.22 plate 4 Compound 141 4310 114.04 1.61E+07 16.48 plate 4 Compound 142 5091 134.71 3.74E+07 38.22 plate 4 Compound 35 6601 174.65 8.50E+07 86.77 plate 4 Compound 143 3582 94.79 2.17E+07 22.14 plate 4 Compound 144 6787 179.57 5.45E+07 55.69 plate 4 Compound 145 3752 99.29 2.23E+07 22.81 plate 4 Compound 146 2554 67.59 1.83E+07 18.71 plate 4 Compound 112 3289 87.03 1.48E+07 15.11 plate 4 Compound 113 3819 101.06 2.34E+07 23.93 plate 4 Compound 114 1259 33.32 1.34E+07 13.67 plate 4 Compound 22 5517 145.98 7.09E+07 72.39 plate 4 Compound 150 5104 135.04 3.34E+07 34.11 plate 5 no Activin A (with Wnt3a) 7159 116.70 8.12E+06 2.51 plate 5 Activin A/Wnt3a 10619 173.09 3.23E+08 100.00 plate 5 Compound 151 2785 45.39 −1.03E+06  −0.32 plate 5 Compound 152 4693 76.50 −3.08E+06  −0.95 plate 5 Compound 153 9718 158.40 −1.20E+06  −0.37 plate 5 Compound 154 3479 56.70 −1.97E+06  −0.61 plate 5 Compound 155 9343 152.28 −3.45E+06  −1.07 plate 5 Compound 156 3813 62.16 −2.58E+05  −0.08 plate 6 no Activin A (with Wnt3a) 3264 68.37 2.52E+06 0.80 plate 6 Activin A/Wnt3a 9902 207.40 3.14E+08 100.00 plate 6 Compound 157 2480 51.94 −1.22E+06  −0.39 plate 6 Compound 158 5271 110.41 −1.30E+06  −0.41 plate 6 Compound 159 6478 135.68 −1.84E+06  −0.59 plate 6 Compound 160 4212 88.21 1.30E+05 0.04 plate 6 Compound 161 2439 51.09 −9.20E+05  −0.29 plate 6 Compound 162 1260 26.39 −1.35E+06  −0.43 plate 7 no Activin A (with Wnt3a) 9545 156.12 −4.87E+06  −0.99 plate 7 Activin A/Wnt3a 20064 328.17 4.92E+08 100.00 plate 7 Compound 163 16557 270.81 −7.31E+06  −1.49 plate 7 Compound 164 16472 269.42 −7.37E+06  −1.50 plate 7 Compound 165 3015 49.32 −7.34E+06  −1.49 plate 7 Compound 166 13845 226.45 −7.98E+06  −1.62 plate 7 Compound 167 10325 168.87 −7.35E+06  −1.49 plate 7 Compound 168 14139 231.26 −6.49E+06  −1.32 plate 7 Compound 169 4468 73.08 −6.38E+06  −1.30 plate 8 no Activin A (with Wnt3a) 6868 179.83 −2.31E+06  −0.52 plate 8 Activin A/Wnt3a 18575 486.35 4.47E+08 100.00 plate 8 Compound 170 13140 344.04 −4.13E+06  −0.93 plate 8 Compound 171 10894 285.22 −2.61E+06  −0.58 plate 8 Compound 172 3416 89.44 −4.72E+06  −1.06 plate 8 Compound 173 8815 230.81 −4.25E+06  −0.95 plate 8 Compound 174 11760 307.91 −3.33E+06  −0.75 plate 8 Compound 175 5 0.13 −4.91E+06  −1.10 plate 8 Compound 176 10139 265.47 −4.73E+06  −1.06 plate 8 Compound 177 9994 261.68 −2.95E+06  −0.66 plate 8 Compound 178 8998 235.58 −3.74E+06  −0.84 plate 5 no Activin A (with Wnt3a) 7159 67.42 8.12E+06 2.51 plate 5 Activin A/Wnt3a 10619 100.00 3.23E+08 100.00 plate 5 Compound 21 4719 44.44 −1.96E+06  −0.61 plate 5 Compound 22 2036 19.18 −1.79E+06  −0.55 plate 5 Compound 23 2563 24.13 −1.56E+06  −0.48 plate 5 Compound 24 4470 42.09 −7.05E+05  −0.22 plate 5 Compound 24 6085 57.30 −3.08E+06  −0.95 plate 5 Compound 26 7276 68.52 −2.38E+06  −0.74 plate 5 Compound 27 4588 43.20 −5.63E+05  −0.17 plate 5 Compound 28 2682 25.26 −1.37E+06  −0.43 plate 5 Compound 29 5778 54.41 −1.94E+06  −0.60 plate 5 Compound 30 620 5.84 −5.05E+06  −1.56 plate 5 Compound 31 3419 32.19 −1.42E+06  −0.44 plate 6 no Activin A (with Wnt3a) 3264 69.07 2.52E+06 0.80 plate 6 Activin A/Wnt3a 9902 209.51 3.14E+08 100.00 plate 6 Compound 32 2142 45.32 −1.33E+06  −0.42 plate 6 Compound 33 5564 117.73 −8.63E+05  −0.27 plate 6 Compound 34 5927 125.41 −2.01E+06  −0.64 plate 6 Compound 35 10068 213.01 −2.15E+06  −0.68 plate 6 Compound 36 5170 109.39 −1.22E+06  −0.39 plate 6 Compound 37 3098 65.55 1.91E+06 0.61 plate 6 Compound 38 1537 32.52 4.48E+04 0.01 plate 6 Compound 39 3650 77.23 −2.01E+06  −0.64 plate 6 Compound 40 5817 123.07 4.91E+05 0.16 plate 6 Compound 64 4359 92.23 −1.07E+05  −0.03 plate 6 Compound 30 4035 85.38 2.09E+06 0.66 plate 6 Compound 65 3279 69.37 −5.63E+05  −0.18 plate 6 Compound 67 2698 57.08 −1.95E+06  −0.62 plate 7 no Activin A (with Wnt3a) 9545 321.22 −4.87E+06  −0.99 plate 7 Activin A/Wnt3a 20064 675.20 4.92E+08 100.00 plate 7 Compound 68 10894 366.62 −5.15E+06  −1.05 plate 7 Compound 69 9734 327.58 −3.97E+06  −0.81 plate 7 Compound 70 16736 563.21 −6.51E+06  −1.32 plate 7 Compound 71 17999 605.71 −7.38E+06  −1.50 plate 7 Compound 72 7309 245.96 −6.47E+06  −1.32 plate 7 Compound 73 8888 299.10 −3.03E+06  −0.62 plate 7 Compound 74 11496 386.85 −2.67E+06  −0.54 plate 7 Compound 75 9739 327.74 −7.75E+06  −1.57 plate 7 Compound 76 14439 485.89 −4.19E+06  −0.85 plate 7 Compound 77 12331 414.95 −6.03E+06  −1.22 plate 7 Compound 78 9702 326.49 −6.57E+06  −1.33 plate 7 Compound 79 8535 287.22 −6.92E+06  −1.41 plate 8 no Activin A (with Wnt3a) 6868 295.49 −2.31E+06  −0.52 plate 8 Activin A/Wnt3a 18575 799.17 4.47E+08 100.00 plate 8 Compound 80 13939 599.68 −4.23E+06  −0.95 plate 8 Compound 81 10466 450.29 −4.91E+06  −1.10 plate 8 Compound 82 10323 444.14 −4.90E+06  −1.10 plate 8 Compound 83 14619 628.95 1.48E+06 0.33 plate 8 Compound 84 14105 606.84 −4.44E+06  −0.99 plate 8 Compound 85 12172 523.66 −3.48E+06  −0.78 plate 8 Compound 86 7218 310.54 −4.22E+06  −0.94 plate 8 Compound 87 5383 231.58 −4.07E+06  −0.91 plate 8 Compound 88 10419 448.27 −4.27E+06  −0.96 plate 8 Compound 89 11780 506.83 −3.94E+06  −0.88 plate 8 Compound 90 7002 301.25 −1.54E+06  −0.35 plate 8 Compound 91 6224 267.78 −4.53E+06  −1.01

TABLE 2 Cell Number Sox17 Intensity Compound # % of positive control % of positive control Compound 17 133.8 −0.7 Compound 95 195.0 40.7 Compound 138 185.7 31.4 Compound 87 170.7 50.4 Compound 144 163.2 55.7 Compound 35 158.7 86.8 Compound 30 153.1 43.1 Compound 105 151.0 51.0 Compound 39 147.0 35.2 Compound 104 142.5 50.0 Compound 29 136.0 34.5 Compound 22 132.7 72.4 Compound 37 129.3 29.1 Compound 134 126.9 35.0 Compound 150 122.7 34.1 Compound 142 122.4 38.2 Compound 136 117.4 32.7 Compound 80 115.2 38.6 Compound 34 114.8 44.5 Compound 102 113.5 21.3 Compound 89 110.7 21.4 Compound 105 105.8 30.7 Compound 78 105.5 31.0 Compound 141 103.6 16.5 Compound 110 102.5 25.7 Compound 133 102.0 32.9

TABLE 3A Cell Number Sox17 Expression % of % of AverageTotal positive Average Total positive Compound # Treatments Cell Number control Intensity control none no Activin A, with Wnt3a 23253 124.16 1.97E+07 10.59 none Activin A/Wnt3a 18728 100.00 1.86E+08 100.00 Compound 17 no AA (with Wnt3a) EGF + FGF4 21445 114.51 3.43E+07 18.48 none no Activin A, with Wnt3a 23253 124.16 1.97E+07 10.59 none Activin A/Wnt3a 18728 100.00 1.86E+08 100.00 Compound 22 no AA (with Wnt3a) EGF + FGF4 18336 97.91 3.72E+07 20.05 Compound 34 no AA (with Wnt3a) EGF + FGF4 18891 100.87 3.26E+07 17.55 Compound 29 no AA (with Wnt3a) EGF + FGF4 20221 107.97 2.83E+07 15.27 Compound 39 no AA (with Wnt3a) EGF + FGF4 17095 91.28 2.82E+07 15.19 Compound 37 no AA (with Wnt3a) EGF + FGF4 15605 83.32 2.67E+07 14.37 Compound 35 no AA (with Wnt3a) EGF + FGF4 23823 127.20 2.54E+07 13.69 Compound 80 no AA (with Wnt3a) EGF + FGF4 19864 106.07 2.33E+07 12.54 Compound 141 no AA (with Wnt3a) EGF + FGF4 17719 94.61 2.24E+07 12.04 Compound 30 no AA (with Wnt3a) EGF + FGF4 18063 96.45 2.18E+07 11.73 Compound 150 no AA (with Wnt3a) EGF + FGF4 16833 89.88 2.16E+07 11.63 Compound 144 no AA (with Wnt3a) EGF + FGF4 17100 91.31 2.04E+07 11.01 Compound 104 no AA (with Wnt3a) EGF + FGF4 17863 95.38 1.89E+07 10.19 Compound 142 no AA (with Wnt3a) EGF + FGF4 18955 101.21 1.84E+07 9.90 Compound 110 no AA (with Wnt3a) EGF + FGF4 17534 93.62 1.76E+07 9.45 Compound 78 no AA (with Wnt3a) EGF + FGF4 17703 94.52 1.71E+07 9.23 Compound 133 no AA (with Wnt3a) EGF + FGF4 16521 88.22 1.67E+07 8.97 Compound 87 no AA (with Wnt3a) EGF + FGF4 16495 88.07 1.55E+07 8.33 Compound 95 no AA (with Wnt3a) EGF + FGF4 16900 90.24 1.43E+07 7.72 Compound 136 no AA (with Wnt3a) EGF + FGF4 19167 102.34 7.91E+06 4.26 Compound 105 no AA (with Wnt3a) EGF + FGF4 15217 81.25 7.45E+06 4.01 Compound 134 no AA (with Wnt3a) EGF + FGF4 17208 91.88 7.40E+06 3.99 Compound 138 no AA (with Wnt3a) EGF + FGF4 16695 89.14 6.65E+06 3.58 Compound 89 no AA (with Wnt3a) EGF + FGF4 14652 78.24 3.89E+06 2.10 Compound 90 no AA (with Wnt3a) EGF + FGF4 15903 84.92 3.53E+06 1.90 Compound 102 no AA (with Wnt3a) EGF + FGF4 12943 69.11 2.85E+05 0.15 none no Activin A, with Wnt3a 23253 124.16 1.97E+07 10.59 none Activin A/Wnt3a 18728 100.00 1.86E+08 100.00 Compound 35 no AA (with Wnt3a) EGF + FGF4 18294 97.68 1.99E+07 10.70

TABLE 3B Cell Number Sox17 Intensity Compound # % of positive control % of positive control Compound 22 97.91 20.05 Compound 34 100.87 17.55 Compound 29 107.97 15.27 Compound 39 91.28 15.19 Compound 37 83.32 14.37 Compound 35 127.20 13.69

TABLE 4 Cell Number Sox17 Expression Avg. % of Avg. % of Total Cell positive Total positive Compound # Treatments Number control Intensity control none no Activin A (with Wnt3a) 7107 67.96 −1.27E+07  −7.94 none Activin A/Wnt3a 10459 100.00 1.60E+08 100.00 Compound 17 no AA (with Wnt3a) EGF 6942 73.43 1.27E+06 0.74 Compound 17 no AA (with Wnt3a) EGF + FGF4 5738 60.69 3.14E+06 1.83 Compound 17 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB 4453 47.10 9.30E+05 0.54 Compound 17 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB + 10391 109.91 8.92E+06 5.20 Muscimol Compound 17 no AA (with Wnt3a) EGF + PDGF-A + VEGF 5728 60.59 2.14E+06 1.24 Compound 17 no AA (with Wnt3a) FGF4 + PDGF-A + VEGF 13198 139.59 1.29E+07 7.54 Compound 17 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + 10480 110.85 8.97E+06 5.23 VEGF Compound 17 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + 13649 144.37 1.45E+07 8.43 Muscimol none no Activin A (with Wnt3a) 3117 34.86 −1.41E+06  −0.72 none Activin A/Wnt3a 8942 100.00 1.95E+08 100.00 Compound 35 no AA (with Wnt3a) EGF 19334 216.23 6.62E+07 33.86 Compound 35 no AA (with Wnt3a) PDGF-AB 16662 186.34 4.95E+07 25.33 Compound 35 no AA (with Wnt3a) PDGF-A 16885 188.84 4.48E+07 22.94 Compound 35 no AA (with Wnt3a) VEGF 18263 204.25 3.51E+07 17.98 Compound 35 no AA (with Wnt3a) FGF4 4410 49.32 3.33E+07 17.04 Compound 35 no AA (with Wnt3a) Muscimol 18867 211.00 2.61E+07 13.35 Compound 35 no AA (with Wnt3a) PDGF-C 16642 186.12 1.85E+07 9.46 Compound 35 no AA (with Wnt3a) PDGF-D 17618 197.03 1.84E+07 9.41 Compound 35 no AA (with Wnt3a) PDGF-B 14168 158.46 1.52E+07 7.76 Compound 35 no AA (with Wnt3a) PD98059 18877 211.11 1.30E+07 6.64 Compound 35 no AA (with Wnt3a) BMP1 18849 210.81 1.29E+07 6.59 Compound 35 no AA (with Wnt3a) LY294002 18374 205.49 1.03E+07 5.28 Compound 35 no AA (with Wnt3a) BMP4 16748 187.31 8.97E+06 4.59 Compound 35 no AA (with Wnt3a) BMP2 16218 181.38 8.89E+06 4.55 Compound 35 no AA (with Wnt3a) BMP7 20111 224.91 8.05E+06 4.12 Compound 35 no AA (with Wnt3a) U0124 16539 184.97 7.54E+06 3.86 Compound 35 no AA (with Wnt3a) BMP6 17838 199.50 7.32E+06 3.75 Compound 35 no AA (with Wnt3a) BMP2/7 12042 134.67 7.08E+06 3.62 Compound 35 no AA (with Wnt3a) bicuculline 19312 215.98 1.95E+06 1.00 Compound 35 no AA (with Wnt3a) U0126 19961 223.24 −5.75E+05  −0.29 Compound 35 no AA (with Wnt3a) Butyrate 14238 159.24 −1.85E+06  −0.94 none no Activin A (with Wnt3a) 6049 45.2 −1.31E+07  −5.2 none Activin A/Wnt3a 13392 100.0 2.50E+08 100.0 Compound 20 EGF, FGF, PDGF-A, VEGF, 9434 70.4 1.48E+08 59.1 PDGF-D, muscimol, GDF-8 Compound 17 EGF, FGF, PDGF-A, VEGF, 7988 59.6 1.13E+08 45.0 PDGF-D, muscimol, GDF-8 Compound 16 EGF, FGF, PDGF-A, VEGF, 8303 62.0 9.20E+07 36.7 PDGF-D, muscimol, GDF-8 Compound 13 EGF, FGF, PDGF-A, VEGF, 7045 52.6 7.22E+07 28.8 PDGF-D, muscimol, GDF-8 Compound 19 EGF, FGF, PDGF-A, VEGF, 7799 58.2 6.82E+07 27.2 PDGF-D, muscimol, GDF-8 Compound 92 EGF, FGF, PDGF-A, VEGF, 5886 44.0 5.63E+07 22.5 PDGF-D, muscimol, GDF-8 Compound 93 EGF, FGF, PDGF-A, VEGF, 5463 40.8 4.38E+07 17.5 PDGF-D, muscimol, GDF-8 Compound 94 EGF, FGF, PDGF-A, VEGF, 5100 38.1 4.18E+07 16.7 PDGF-D, muscimol, GDF-8 Compound 95 EGF, FGF, PDGF-A, VEGF, 4510 33.7 3.32E+07 13.3 PDGF-D, muscimol, GDF-8 Compound 96 EGF, FGF, PDGF-A, VEGF, 4570 34.1 3.09E+07 12.3 PDGF-D, muscimol, GDF-8 Compound 97 EGF, FGF, PDGF-A, VEGF, 4561 34.1 2.15E+07 8.6 PDGF-D, muscimol, GDF-8 Compound 98 EGF, FGF, PDGF-A, VEGF, 3176 23.7 9.86E+06 3.9 PDGF-D, muscimol, GDF-8 Compound 99 EGF, FGF, PDGF-A, VEGF, 1209 9.0 −1.56E+07  −6.2 PDGF-D, muscimol, GDF-8 none no Activin A (with Wnt3a) 15494 98.0 −1.25E+07  −4.4 none Activin A/Wnt3a 15807 100.0 2.86E+08 100.0 Compound 18 EGF, FGF, PDGF-A, VEGF, 8742 55.3 1.01E+08 35.4 PDGF-D, muscimol, GDF-8 Compound 14 EGF, FGF, PDGF-A, VEGF, 8464 53.5 8.33E+07 29.1 PDGF-D, muscimol, GDF-8 Compound 15 EGF, FGF, PDGF-A, VEGF, 7234 45.8 7.95E+07 27.8 PDGF-D, muscimol, GDF-8 Compound 100 EGF, FGF, PDGF-A, VEGF, 6805 43.0 5.88E+07 20.6 PDGF-D, muscimol, GDF-8 Compound 101 EGF, FGF, PDGF-A, VEGF, 5668 35.9 5.34E+07 18.7 PDGF-D, muscimol, GDF-8 Compound 102 EGF, FGF, PDGF-A, VEGF, 6195 39.2 5.29E+07 18.5 PDGF-D, muscimol, GDF-8 Compound 103 EGF, FGF, PDGF-A, VEGF, 7545 47.7 5.13E+07 18.0 PDGF-D, muscimol, GDF-8 Compound 104 EGF, FGF, PDGF-A, VEGF, 4757 30.1 4.58E+07 16.0 PDGF-D, muscimol, GDF-8 Compound 105 EGF, FGF, PDGF-A, VEGF, 6285 39.8 4.29E+07 15.0 PDGF-D, muscimol, GDF-8 Compound 106 EGF, FGF, PDGF-A, VEGF, 5622 35.6 2.86E+07 10.0 PDGF-D, muscimol, GDF-8 Compound 107 EGF, FGF, PDGF-A, VEGF, 3951 25.0 1.72E+07 6.0 PDGF-D, muscimol, GDF-8 Compound 108 EGF, FGF, PDGF-A, VEGF, 3226 20.4 1.58E+07 5.5 PDGF-D, muscimol, GDF-8 Compound 109 EGF, FGF, PDGF-A, VEGF, 3473 22.0 1.46E+07 5.1 PDGF-D, muscimol, GDF-8 Compound 110 EGF, FGF, PDGF-A, VEGF, 3703 23.4 1.32E+07 4.6 PDGF-D, muscimol, GDF-8 Compound 111 EGF, FGF, PDGF-A, VEGF, 2918 18.5 1.22E+07 4.3 PDGF-D, muscimol, GDF-8 Compound 112 EGF, FGF, PDGF-A, VEGF, 2975 18.8 1.04E+07 3.6 PDGF-D, muscimol, GDF-8 Compound 113 EGF, FGF, PDGF-A, VEGF, 2910 18.4 9.18E+06 3.2 PDGF-D, muscimol, GDF-8 Compound 114 EGF, FGF, PDGF-A, VEGF, 2734 17.3 6.13E+06 2.1 PDGF-D, muscimol, GDF-8 Compound 115 EGF, FGF, PDGF-A, VEGF, 2169 13.7 3.77E+06 1.3 PDGF-D, muscimol, GDF-8 Compound 116 EGF, FGF, PDGF-A, VEGF, 3107 19.7 3.52E+06 1.2 PDGF-D, muscimol, GDF-8 Compound 117 EGF, FGF, PDGF-A, VEGF, 3343 21.1 5.35E+05 0.2 PDGF-D, muscimol, GDF-8 Compound 118 EGF, FGF, PDGF-A, VEGF, 3034 19.2 2.37E+05 0.1 PDGF-D, muscimol, GDF-8 Compound 119 EGF, FGF, PDGF-A, VEGF, 2263 14.3 −1.66E+06  −0.6 PDGF-D, muscimol, GDF-8 Compound 120 EGF, FGF, PDGF-A, VEGF, 1771 11.2 −5.57E+06  −2.0 PDGF-D, muscimol, GDF-8 Compound 121 EGF, FGF, PDGF-A, VEGF, 1136 7.2 −1.79E+07  −6.3 PDGF-D, muscimol, GDF-8 Compound 122 EGF, FGF, PDGF-A, VEGF, 2021 12.8 −2.09E+07  −7.3 PDGF-D, muscimol, GDF-8

TABLE 5 Cell Number Sox17 Expression Avg. % of Avg. % of Total Cell positive Total positive Compound # Treatments Number control Intensity control none no Activin A (with Wnt3a) 7107 67.96 −1.27E+07  −7.94 none Activin A/Wnt3a 10459 100.00 1.60E+08 100.00 Compound 17 no AA (with Wnt3a) EGF 6942 73.43 1.27E+06 0.74 Compound 17 no AA (with Wnt3a) EGF + FGF4 5738 60.69 3.14E+06 1.83 Compound 17 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB 4453 47.10 9.30E+05 0.54 Compound 17 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB + Muscimol 10391 109.91 8.92E+06 5.20 Compound 17 no AA (with Wnt3a) EGF + PDGF-A + VEGF 5728 60.59 2.14E+06 1.24 Compound 17 no AA (with Wnt3a) FGF4 + PDGF-A + VEGF 13198 139.59 1.29E+07 7.54 Compound 17 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + VEGF 10480 110.85 8.97E+06 5.23 Compound 17 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + Muscimol 13649 144.37 1.45E+07 8.43 none no Activin A (with Wnt3a) 7107 67.96 −1.27E+07  −7.94 none Activin A/Wnt3a 10459 100.00 1.60E+08 100.00 Compound 35 no AA (with Wnt3a) EGF 23887 228.40 −1.01E+07  −6.32 Compound 35 no AA (with Wnt3a) EGF + FGF4 21268 203.36 1.36E+06 0.85 Compound 35 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB 17611 168.39 1.28E+07 8.03 Compound 35 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB + Muscimol 17949 171.62 1.54E+06 0.96 Compound 35 no AA (with Wnt3a) EGF + PDGF-A + VEGF 23242 222.23 1.23E+07 7.72 Compound 35 no AA (with Wnt3a) FGF4 + PDGF-A + VEGF 16068 153.63 3.92E+07 24.57 Compound 35 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + VEGF 16132 154.25 9.11E+07 57.04 Compound 35 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + Muscimol 15457 147.80 6.89E+07 43.15 Compound 29 no AA (with Wnt3a) EGF 1971 18.84 −1.44E+07  −9.00 Compound 29 no AA (with Wnt3a) EGF + FGF4 7436 71.10 −4.35E+06  −2.72 Compound 29 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB 6535 62.48 −7.52E+06  −4.71 Compound 29 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB + Muscimol 1376 13.15 −1.42E+07  −8.91 Compound 29 no AA (with Wnt3a) EGF + PDGF-A + VEGF 8880 84.91 −8.53E+06  −5.34 Compound 29 no AA (with Wnt3a) FGF4 + PDGF-A + VEGF 8146 77.89 −4.82E+06  −3.02 Compound 29 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + VEGF 8858 84.70 −7.15E+06  −4.48 Compound 29 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + Muscimol 10071 96.30 2.95E+06 1.85 Compound 37 no AA (with Wnt3a) EGF 7966 76.17 −1.19E+07  −7.42 Compound 37 no AA (with Wnt3a) EGF + FGF4 6932 66.28 −4.62E+06  −2.89 Compound 37 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB 7473 71.46 −2.61E+06  −1.63 Compound 37 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB + Muscimol 7914 75.67 −1.91E+06  −1.20 Compound 37 no AA (with Wnt3a) EGF + PDGF-A + VEGF 12956 123.88 −1.25E+07  −7.82 Compound 37 no AA (with Wnt3a) FGF4 + PDGF-A + VEGF 6731 64.36 −1.10E+07  −6.89 Compound 37 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + VEGF 8778 83.93 1.39E+05 0.09 Compound 37 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + Muscimol 5821 55.66 −1.22E+07  −7.64 Compound 34 no AA (with Wnt3a) EGF 13062 124.89 2.78E+07 17.39 Compound 34 no AA (with Wnt3a) EGF + FGF4 13133 125.58 1.23E+08 76.85 Compound 34 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB 12532 119.83 1.09E+08 68.41 Compound 34 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB + Muscimol 15811 151.18 6.90E+06 4.32 Compound 34 no AA (with Wnt3a) EGF + PDGF-A + VEGF 11801 112.84 4.04E+06 2.53 Compound 34 no AA (with Wnt3a) FGF4 + PDGF-A + VEGF 15262 145.93 1.15E+07 7.18 Compound 34 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + VEGF 12901 123.36 5.01E+07 31.35 Compound 34 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + Muscimol 12208 116.72 5.56E+07 34.83 none no Activin A (with Wnt3a) 10224 108.14 7.36E+05 0.43 none Activin A/Wnt3a 9455 100.00 1.72E+08 100.00 Compound 39 no AA (with Wnt3a) EGF 11615 122.85 1.49E+05 0.09 Compound 39 no AA (with Wnt3a) EGF + FGF4 10456 110.59 5.11E+06 2.98 Compound 39 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB 9972 105.47 1.62E+06 0.94 Compound 39 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB + Muscimol 10540 111.48 2.22E+06 1.29 Compound 39 no AA (with Wnt3a) EGF + PDGF-A + VEGF 17050 180.34 4.84E+06 2.82 Compound 39 no AA (with Wnt3a) FGF4 + PDGF-A + VEGF 8856 93.67 7.01E+05 0.41 Compound 39 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + VEGF 7973 84.33 5.30E+06 3.09 Compound 39 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + Muscimol 9103 96.28 7.32E+05 0.43 Compound 22 no AA (with Wnt3a) EGF 14105 149.19 1.75E+06 1.02 Compound 22 no AA (with Wnt3a) EGF + FGF4 12971 137.19 1.04E+07 6.05 Compound 22 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB 16580 175.36 8.60E+06 5.01 Compound 22 no AA (with Wnt3a) EGF + FGF4 + PDGF-AB + Muscimol 14676 155.23 5.61E+06 3.27 Compound 22 no AA (with Wnt3a) EGF + PDGF-A + VEGF 20372 215.48 4.99E+06 2.91 Compound 22 no AA (with Wnt3a) FGF4 + PDGF-A + VEGF 12277 129.85 4.90E+06 2.86 Compound 22 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + VEGF 12522 132.44 7.88E+06 4.59 Compound 22 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + Muscimol 11610 122.80 1.33E+07 7.77

TABLE 6 Cell Number Sox17 Expression Average % of Average % of Total Cell positive Total positive Compound # Treatments Number control Intensity control none no Activin A (with Wnt3a) 477 6.64 7.4E+04 0.09 none Activin A/Wnt3a 7185 100.00 8.0E+07 100.00 Compound 34 no AA (with Wnt3a) none 4611 64.18 1.4E+07 17.21 Compound 34 no AA (with Wnt3a) EGF 6145 85.53 1.5E+07 19.18 Compound 34 no AA (with Wnt3a) FGF4 5323 74.09 2.7E+07 33.75 Compound 34 no AA (with Wnt3a) PDGF-D 5017 69.84 1.5E+07 18.76 Compound 34 no AA (with Wnt3a) PDGF-A 4175 58.11 1.1E+07 13.43 Compound 34 no AA (with Wnt3a) VEGF 4713 65.60 1.0E+07 12.49 Compound 34 no AA (with Wnt3a) GDF-8 6354 88.44 7.1E+07 88.59 Compound 34 no AA (with Wnt3a) Muscimol 7286 101.41 3.1E+07 38.38 Compound 34 no AA (with Wnt3a) PDGF-D + VEGF 5030 70.01 1.2E+07 14.58 Compound 34 no AA (with Wnt3a) VEGF + Muscimol 776 10.81 1.3E+06 1.56 Compound 34 no AA (with Wnt3a) PDGF-D + Muscimol 3490 48.57 6.5E+06 8.02 Compound 34 no AA (with Wnt3a) GDF-8 + PDGF-D 6889 95.88 5.8E+07 72.59 Compound 34 no AA (with Wnt3a) PDGF-D + Muscimol + VEGF 2133 29.68 2.7E+06 3.32 Compound 34 no AA (with Wnt3a) GDF-8 + PDGF-D + VEGF 5585 77.74 6.6E+07 81.75 Compound 34 no AA (with Wnt3a) GDF-8 + VEGF + Muscimol 6083 84.67 5.6E+07 69.62 Compound 34 no AA (with Wnt3a) GDF-8 + PDGF-D + VEGF + Muscimol 9455 131.60 9.6E+07 119.24 Compound 34 no AA, no Wnt3a EGF + FGF4 + PDGF-A + VEGF + 4757 66.21 3.9E+07 48.77 PDGF-D + Muscimol + GDF-8 Compound 34 no AA (with Wnt3a) EGF + FGF4 + PDGF-A + VEGF + 6028 83.90 7.0E+07 87.44 PDGF-D + Muscimol + GDF-8

TABLE 7 Cell Number Sox17 Expression Avg. % of Average % of Total Cell positive Total positive Plate Treatment Compound # Number control Intensity control 1 no Activin A (with Wnt3a) none 6049 45.2 −1.31E+07  −5.2 1 Activin A/Wnt3a none 13392 100.0 2.50E+08 100.0 1 EGF, FGF, PDGF-A, VEGF, Compound 18 13037 97.3 1.63E+08 65.2 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 14 9344 69.8 1.23E+08 49.0 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 15 8448 63.1 8.64E+07 34.5 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 16 5498 41.1 6.56E+07 26.2 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 64 5063 37.8 5.88E+07 23.5 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 65 4788 35.8 4.57E+07 18.2 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 66 8129 60.7 3.53E+07 14.1 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 67 6791 50.7 3.18E+07 12.7 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 68 3456 25.8 2.30E+07 9.2 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 69 3995 29.8 1.69E+07 6.8 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 70 474 3.5 −1.80E+07  −7.2 PDGF-D, muscimol, GDF-8 2 no Activin A (with Wnt3a) none 15494 98.0 −1.25E+07  −4.4 2 Activin A/Wnt3a none 15807 100.0 2.86E+08 100.0 2 EGF, FGF, PDGF-A, VEGF, Compound 19 8425 53.3 1.19E+08 41.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 13 9123 57.7 1.13E+08 39.7 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 71 6048 38.3 5.51E+07 19.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 72 6060 38.3 5.46E+07 19.1 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 73 5545 35.1 3.99E+07 14.0 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 74 10898 68.9 3.91E+07 13.7 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 75 4117 26.0 3.01E+07 10.5 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 76 3825 24.2 2.74E+07 9.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 77 5928 37.5 2.44E+07 8.5 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 78 3303 20.9 2.03E+07 7.1 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 79 4767 30.2 1.85E+07 6.5 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 80 2194 13.9 1.22E+07 4.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 81 2920 18.5 9.16E+05 0.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 82 1819 11.5 −1.05E+07  −3.7 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 83 2153 13.6 −1.19E+07  −4.2 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 84 58 0.4 −2.94E+07  −10.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 85 57 0.4 −3.03E+07  −10.6 PDGF-D, muscimol, GDF-8 1 no Activin A (with Wnt3a) none 6049 45.2 −1.31E+07  −5.2 1 Activin A/Wnt3a none 13392 100.0 2.50E+08 100.0 1 EGF, FGF, PDGF-A, VEGF, Compound 20 9434 70.4 1.48E+08 59.1 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 17 7988 59.6 1.13E+08 45.0 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 16 8303 62.0 9.20E+07 36.7 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 13 7045 52.6 7.22E+07 28.8 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 19 7799 58.2 6.82E+07 27.2 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 92 5886 44.0 5.63E+07 22.5 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 93 5463 40.8 4.38E+07 17.5 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 94 5100 38.1 4.18E+07 16.7 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 95 4510 33.7 3.32E+07 13.3 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 96 4570 34.1 3.09E+07 12.3 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 97 4561 34.1 2.15E+07 8.6 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 98 3176 23.7 9.86E+06 3.9 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 99 1209 9.0 −1.56E+07  −6.2 PDGF-D, muscimol, GDF-8 2 no Activin A (with Wnt3a) none 15494 98.0 −1.25E+07  −4.4 2 Activin A/Wnt3a none 15807 100.0 2.86E+08 100.0 2 EGF, FGF, PDGF-A, VEGF, Compound 18 8742 55.3 1.01E+08 35.4 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 14 8464 53.5 8.33E+07 29.1 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 15 7234 45.8 7.95E+07 27.8 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 100 6805 43.0 5.88E+07 20.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 101 5668 35.9 5.34E+07 18.7 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 102 6195 39.2 5.29E+07 18.5 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 103 7545 47.7 5.13E+07 18.0 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 104 4757 30.1 4.58E+07 16.0 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 105 6285 39.8 4.29E+07 15.0 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 106 5622 35.6 2.86E+07 10.0 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 107 3951 25.0 1.72E+07 6.0 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 108 3226 20.4 1.58E+07 5.5 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 109 3473 22.0 1.46E+07 5.1 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 110 3703 23.4 1.32E+07 4.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 111 2918 18.5 1.22E+07 4.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 112 2975 18.8 1.04E+07 3.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 113 2910 18.4 9.18E+06 3.2 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 114 2734 17.3 6.13E+06 2.1 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 115 2169 13.7 3.77E+06 1.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 116 3107 19.7 3.52E+06 1.2 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 117 3343 21.1 5.35E+05 0.2 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 118 3034 19.2 2.37E+05 0.1 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 119 2263 14.3 −1.66E+06  −0.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 120 1771 11.2 −5.57E+06  −2.0 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 121 1136 7.2 −1.79E+07  −6.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 122 2021 12.8 −2.09E+07  −7.3 PDGF-D, muscimol, GDF-8 1 no Activin A (with Wnt3a) none 6049 45.2 −1.31E+07  −5.2 1 Activin A/Wnt3a none 13392 100.0 2.50E+08 100.0 1 EGF, FGF, PDGF-A, VEGF, Compound 19 15878 118.6 2.67E+08 106.5 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 24 12714 94.9 2.46E+08 98.2 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 23 12165 90.8 2.15E+08 86.0 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 21 12640 94.4 1.65E+08 65.9 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 13 11491 85.8 1.61E+08 64.3 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 30 11396 85.1 1.34E+08 53.4 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 36 7964 59.5 9.47E+07 37.8 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 32 8066 60.2 9.29E+07 37.1 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 26 7415 55.4 8.30E+07 33.1 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 17 6994 52.2 7.76E+07 31.0 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 31 6957 51.9 6.59E+07 26.3 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 179 3573 26.7 2.43E+07 9.7 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 180 922 6.9 −2.20E+07  −8.8 PDGF-D, muscimol, GDF-8 1 EGF, FGF, PDGF-A, VEGF, Compound 181 8 0.1 −2.68E+07  −10.7 PDGF-D, muscimol, GDF-8 2 no Activin A (with Wnt3a) none 15494 98.0 −1.25E+07  −4.4 2 Activin A/Wnt3a none 15807 100.0 2.86E+08 100.0 2 EGF, FGF, PDGF-A, VEGF, Compound 18 21102 133.5 4.18E+08 146.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 15 15373 97.3 3.74E+08 130.8 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 14 9008 57.0 2.62E+08 91.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 38 9650 61.0 2.46E+08 86.2 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 35 10461 66.2 1.59E+08 55.7 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 16 9064 57.3 1.48E+08 51.8 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 34 8907 56.3 9.99E+07 35.0 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 20 7346 46.5 8.90E+07 31.2 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 27 8044 50.9 8.81E+07 30.8 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 28 7591 48.0 8.77E+07 30.7 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 40 4049 25.6 8.23E+07 28.8 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 33 7485 47.4 8.10E+07 28.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 25 6571 41.6 7.60E+07 26.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 182 7631 48.3 6.74E+07 23.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 183 6777 42.9 5.93E+07 20.8 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 184 5475 34.6 5.44E+07 19.0 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 185 4093 25.9 4.92E+07 17.2 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 186 5274 33.4 4.63E+07 16.2 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 187 5342 33.8 4.02E+07 14.1 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 188 5533 35.0 3.98E+07 13.9 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 189 5928 37.5 3.96E+07 13.9 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 190 4822 30.5 3.90E+07 13.7 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 191 4249 26.9 3.81E+07 13.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 192 5616 35.5 3.54E+07 12.4 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 193 4158 26.3 3.23E+07 11.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 194 3470 22.0 2.96E+07 10.4 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 195 3800 24.0 2.95E+07 10.3 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 196 4619 29.2 2.78E+07 9.7 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 197 4011 25.4 2.45E+07 8.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 198 4367 27.6 1.92E+07 6.7 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 199 3162 20.0 1.20E+07 4.2 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 200 2087 13.2 4.43E+06 1.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 201 1568 9.9 −6.17E+06  −2.2 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 202 5213 33.0 −1.41E+07  −4.9 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 203 7 0.0 −3.04E+07  −10.6 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 204 11 0.1 −3.18E+07  −11.1 PDGF-D, muscimol, GDF-8 2 EGF, FGF, PDGF-A, VEGF, Compound 205 10 0.1 −3.20E+07  −11.2 PDGF-D, muscimol, GDF-8

TABLE 8 Cell Number Sox17 Expression % of % of AverageTotal positive Average Total positive Compound # Cell Number control Intensity control Compound 18 21102 133.5 4.18E+08 146.3 Compound 15 15373 97.3 3.74E+08 130.8 Compound 19 15878 118.6 2.67E+08 106.5 Compound 24 12714 94.9 2.46E+08 98.2 Compound 14 9008 57.0 2.62E+08 91.6 Compound 38 9650 61.0 2.46E+08 86.2 Compound 23 12165 90.8 2.15E+08 86.0 Compound 21 12640 94.4 1.65E+08 65.9 Compound 13 11491 85.8 1.61E+08 64.3 Compound 35 10461 66.2 1.59E+08 55.7 Compound 30 11396 85.1 1.34E+08 53.4 Compound 16 9064 57.3 1.48E+08 51.8 Compound 36 7964 59.5 9.47E+07 37.8 Compound 32 8066 60.2 9.29E+07 37.1 Compound 34 8907 56.3 9.99E+07 35.0 Compound 26 7415 55.4 8.30E+07 33.1 Compound 20 7346 46.5 8.90E+07 31.2 Compound 17 6994 52.2 7.76E+07 31.0 Compound 27 8044 50.9 8.81E+07 30.8 Compound 28 7591 48.0 8.77E+07 30.7 Compound 40 4049 25.6 8.23E+07 28.8 Compound 33 7485 47.4 8.10E+07 28.3 Compound 25 6571 41.6 7.60E+07 26.6 Compound 31 6957 51.9 6.59E+07 26.3 Compound 20 9434 70.4 1.48E+08 59.1 Compound 17 7988 59.6 1.13E+08 45.0 Compound 16 8303 62.0 9.20E+07 36.7 Compound 18 8742 55.3 1.01E+08 35.4 Compound 14 8464 53.5 8.33E+07 29.1 Compound 13 7045 52.6 7.22E+07 28.8 Compound 15 7234 45.8 7.95E+07 27.8 Compound 19 7799 58.2 6.82E+07 27.2

TABLE 9 Cell Number Sox17 Expression Average % of Average % of Treatments Total Cell positive Total positive Plate # Activin A Compound # Growth Factors Number control Intensity control 1 none none none 9164 149.46 −5.91E+06  −5.17 1 10 ng/ml AA none none 6132 100.00 1.52E+06 1.33 1 100 ng/ml AA  none none 9658 157.51 1.14E+08 100.00 1 10 ng/ml AA Compound 22 EGF + FGF4 + PDGF-A + VEGF + 8556 139.53 8.78E+07 76.82 PDGF-D + Muscimol + GDF-8 + Wnt3a 1 10 ng/ml AA Compound 22 EGF + FGF4 + PDGF-AB + VEGF + Wnt3a 7657 124.87 4.70E+07 41.09 1 10 ng/ml AA Compound 22 EGF + FGF4 + PDGF-A + Muscimol + Wnt3a 8100 132.10 4.42E+07 38.65 1 10 ng/ml AA Compound 22 EGF + FGF4 + PDGF-AB + Wnt3a 7975 130.06 3.43E+07 30.03 1 10 ng/ml AA Compound 22 EGF + FGF4 + Wnt3a 9800 159.83 4.59E+07 40.13 1 10 ng/ml AA Compound 22 FGF4 + Wnt3a 6490 105.84 4.28E+07 37.43 1 10 ng/ml AA Compound 22 EGF + Wnt3a 5001 81.55 2.80E+07 24.45 1 10 ng/ml AA Compound 22 Wnt3a 4543 74.09 3.05E+07 26.65 1 10 ng/ml AA Compound 35 EGF + FGF4 + PDGF-A + VEGF + 2522 41.14 −4.86E+06  −4.25 PDGF-D + Muscimol + GDF-8 + Wnt3a 1 10 ng/ml AA Compound 35 EGF + FGF4 + PDGF-AB + VEGF + Wnt3a 3479 56.74 −3.96E+06  −3.46 1 10 ng/ml AA Compound 35 EGF + FGF4 + PDGF-A + Muscimol + Wnt3a 3820 62.29 −1.67E+06  −1.46 1 10 ng/ml AA Compound 35 EGF + FGF4 + PDGF-AB + Wnt3a 3263 53.21 −4.56E+06  −3.99 1 10 ng/ml AA Compound 35 EGF + FGF4 + Wnt3a 2704 44.10 −4.17E+06  −3.65 1 10 ng/ml AA Compound 35 FGF4 + Wnt3a 284 4.64 −7.54E+06  −6.59 1 10 ng/ml AA Compound 35 EGF + Wnt3a 155 2.53 −7.82E+06  −6.84 1 10 ng/ml AA Compound 35 Wnt3a 173 2.83 −7.61E+06  −6.66 1 10 ng/ml AA Compound 29 EGF + FGF4 + PDGF-A + VEGF + 2737 44.63 2.41E+07 21.10 PDGF-D + Muscimol + GDF-8 + Wnt3a 1 10 ng/ml AA Compound 29 EGF + FGF4 + PDGF-AB + VEGF + Wnt3a 2283 37.23 5.59E+06 4.88 1 10 ng/ml AA Compound 29 EGF + FGF4 + PDGF-A + Muscimol + Wnt3a 4676 76.26 2.41E+07 21.11 1 10 ng/ml AA Compound 29 EGF + FGF4 + PDGF-AB + Wnt3a 3964 64.65 2.27E+07 19.89 1 10 ng/ml AA Compound 29 EGF + FGF4 + Wnt3a 1736 28.31 1.98E+06 1.73 1 10 ng/ml AA Compound 29 FGF4 + Wnt3a 2139 34.89 6.98E+06 6.10 1 10 ng/ml AA Compound 29 EGF + Wnt3a 365 5.96 −4.86E+06  −4.25 1 10 ng/ml AA Compound 29 Wnt3a 2090 34.09 4.89E+06 4.28 2 none none none 9325 121.89 −3.35E+06  −3.01 2 10 ng/ml AA none none 5177 67.67 3.89E+06 3.49 2 100 ng/ml AA  none none 7650 100.00 1.11E+08 100.00 2 10 ng/ml AA Compound 34 EGF + FGF4 + PDGF-A + VEGF + 18362 240.02 3.45E+08 309.74 PDGF-D + Muscimol + GDF-8 + Wnt3a 2 10 ng/ml AA Compound 34 EGF + FGF4 + PDGF-AB + VEGF + Wnt3a 15574 203.58 2.59E+08 232.70 2 10 ng/ml AA Compound 34 EGF + FGF4 + PDGF-A + Muscimol + Wnt3a 17890 233.85 2.88E+08 258.30 2 10 ng/ml AA Compound 34 EGF + FGF4 + PDGF-AB + Wnt3a 17875 233.65 2.68E+08 241.07 2 10 ng/ml AA Compound 34 EGF + FGF4 + Wnt3a 14158 185.07 2.40E+08 215.35 2 10 ng/ml AA Compound 34 FGF4 + Wnt3a 13323 174.15 2.19E+08 196.86 2 10 ng/ml AA Compound 34 EGF + Wnt3a 14527 189.89 2.28E+08 204.84 2 10 ng/ml AA Compound 34 Wnt3a 3589 46.91 7.02E+07 63.08 2 10 ng/ml AA Compound 39 EGF + FGF4 + PDGF-A + VEGF + 5738 75.00 2.14E+07 19.24 PDGF-D + Muscimol + GDF-8 + Wnt3a 2 10 ng/ml AA Compound 39 EGF + FGF4 + PDGF-AB + VEGF + Wnt3a 2531 33.08 2.82E+06 2.53 2 10 ng/ml AA Compound 39 EGF + FGF4 + PDGF-A + Muscimol + Wnt3a 2879 37.64 3.61E+06 3.24 2 10 ng/ml AA Compound 39 EGF + FGF4 + PDGF-AB + Wnt3a 2989 39.07 −1.78E+04  −0.02 2 10 ng/ml AA Compound 39 EGF + FGF4 + Wnt3a 734 9.59 −3.93E+06  −3.53 2 10 ng/ml AA Compound 39 FGF4 + Wnt3a 521 6.81 −4.46E+06  −4.01 2 10 ng/ml AA Compound 39 EGF + Wnt3a 211 2.75 −4.54E+06  −4.08 2 10 ng/ml AA Compound 39 Wnt3a 518 6.78 −2.37E+06  −2.13 2 10 ng/ml AA Compound 37 EGF + FGF4 + PDGF-A + VEGF + 5711 74.65 1.21E+07 10.82 PDGF-D + Muscimol + GDF-8 + Wnt3a 2 10 ng/ml AA Compound 37 EGF + FGF4 + PDGF-AB + VEGF + Wnt3a 4767 62.31 −5.16E+05  −0.46 2 10 ng/ml AA Compound 37 EGF + FGF4 + PDGF-A + Muscimol + Wnt3a 4540 59.34 9.23E+05 0.83 2 10 ng/ml AA Compound 37 EGF + FGF4 + PDGF-AB + Wnt3a 4223 55.20 −6.15E+05  −0.55 2 10 ng/ml AA Compound 37 EGF + FGF4 + Wnt3a 3501 45.77 5.60E+05 0.50 2 10 ng/ml AA Compound 37 FGF4 + Wnt3a 3930 51.37 −1.88E+06  −1.69 2 10 ng/ml AA Compound 37 EGF + Wnt3a 1431 18.70 −2.75E+06  −2.47 2 10 ng/ml AA Compound 37 Wnt3a 791 10.34 −2.99E+06  −2.68

TABLE 10 Cell Number Sox17 Expression Average % of Average % of Total Cell positive Total positive Compound # Treatments Number control Intensity control none No Activin A (with Wnt3a) 4273 33.70 4.75E+07 17.49 none Activin A (with Wnt3a) 12676 100.00 2.72E+08 100.00 Compound 34 No AA (without Wnt3a) FGF(50 ng/ml) EGF(50 ng/ml) 13317 105.06 2.01E+08 74.08 Compound 34 No AA (without Wnt3a) FGF(50 ng/ml) EGF(100 ng/ml) 14189 111.93 2.01E+08 73.90 Compound 34 No AA (without Wnt3a) FGF(100 ng/ml) EGF(50 ng/ml) 12616 99.52 1.80E+08 66.21 Compound 34 No AA (without Wnt3a) FGF(100 ng/ml) EGF(100 ng/ml) 8269 65.23 1.13E+08 41.73 Compound 34 No AA (with Wnt3a) none none 11711 92.38 1.65E+08 60.68 Compound 34 No AA (with Wnt3a) none EGF(25 ng/ml) 16052 126.63 2.14E+08 78.82 Compound 34 No AA (with Wnt3a) none EGF(50 ng/ml) 13593 107.23 1.94E+08 71.52 Compound 34 No AA (with Wnt3a) none EGF(100 ng/ml) 13170 103.90 1.93E+08 71.04 Compound 34 No AA (with Wnt3a) FGF(25 ng/ml) none 18433 145.41 2.49E+08 91.72 Compound 34 No AA (with Wnt3a) FGF(25 ng/ml) EGF(25 ng/ml) 18841 148.63 2.60E+08 95.72 Compound 34 No AA (with Wnt3a) FGF(25 ng/ml) EGF(50 ng/ml) 16232 128.05 2.30E+08 84.79 Compound 34 No AA (with Wnt3a) FGF(25 ng/ml) EGF(100 ng/ml) 9309 73.44 1.39E+08 51.00 Compound 34 No AA (with Wnt3a) FGF(50 ng/ml) none 12757 100.64 1.66E+08 61.10 Compound 34 No AA (with Wnt3a) FGF(50 ng/ml) EGF(25 ng/ml) 17720 139.79 2.31E+08 85.01 Compound 34 No AA (with Wnt3a) FGF(50 ng/ml) EGF(50 ng/ml) 16331 128.83 2.26E+08 83.11 Compound 34 No AA (with Wnt3a) FGF(50 ng/ml) EGF(100 ng/ml) 16336 128.87 2.32E+08 85.24 Compound 34 No AA (with Wnt3a) FGF(100 ng/ml) none 19853 156.61 2.59E+08 95.45 Compound 34 No AA (with Wnt3a) FGF(100 ng/ml) EGF(25 ng/ml) 19880 156.83 2.59E+08 95.47 Compound 34 No AA (with Wnt3a) FGF(100 ng/ml) EGF(50 ng/ml) 18166 143.30 2.35E+08 86.30 Compound 34 No AA (with Wnt3a) FGF(100 ng/ml) EGF(100 ng/ml) 11241 88.68 1.55E+08 57.10 none No AA (with Wnt3a) none EGF(50 ng/ml) 5558 43.85 5.01E+07 18.44 none No AA (with Wnt3a) none EGF(100 ng/ml) 6818 53.79 6.42E+07 23.62 none No AA (with Wnt3a) FGF(50 ng/ml) none 8494 67.01 6.62E+07 24.35 none No AA (with Wnt3a) FGF(50 ng/ml) EGF(50 ng/ml) 10138 79.98 7.30E+07 26.87 none No AA (with Wnt3a) FGF(50 ng/ml) EGF(100 ng/ml) 10219 80.62 7.75E+07 28.51 none No AA (with Wnt3a) FGF(100 ng/ml) none 9944 78.45 6.68E+07 24.59 none No AA (with Wnt3a) FGF(100 ng/ml) EGF(50 ng/ml) 11046 87.14 8.17E+07 30.07 none No AA (with Wnt3a) FGF(100 ng/ml) EGF(100 ng/ml) 7695 60.71 6.87E+07 25.28

TABLE 11 Normalized SOX17 Intensity Activin A GDF-8 ng/ml Average SD Average SD 1600 100.00 9.20 100.00 9.00 800 100.00 6.60 84.90 6.30 400 100.00 3.30 72.20 7.50 200 100.00 1.90 51.30 5.30 100 90.70 8.70 32.70 5.10 50 85.20 4.70 17.60 4.80 25 73.10 2.80 5.10 3.60 12.50 50.90 6.20 0.90 0.80 6.25 18.40 4.80 0.70 1.40 3.13 3.00 1.90 0.10 0.20 1.56 0.10 0.00 0.00 0.20 0.00 0.00 0.20 0.30 0.30

TABLE 12 Marker name Catalog # * AFP Hs00173490_m1 CD99 Hs00365982_m1 CD9 Hs00233521_m1 CDH1 Hs00170423_m1 CDH2 Hs00169953_m1 CDX2 Hs00230919_m1 CER1 Hs00193796_m1 CXCR4 Hs00237052_m1 FGF17 Hs00182599_m1 FGF4 Hs00173564_m1 FOXA2 Hs00232764_m1 GAPDH Hs99999905_m1 GATA4 Hs00171403_m1 GATA6 Hs00232018_m1 GSC Hs00418279_m1 HLXB9 Hs00232128_m1 KIT Hs00174029_m1 MIXL1 Hs00430824_g1 NANOG Hs02387400_g1 OTX2 Hs00222238_m1 POU5F1 Hs00742896_s1 SOX17 Hs00751752_s1 SOX7 Hs00846731_s1 T Hs00610080_m1 ALB Hs00609411_m1 AMY2A Hs00420710_g1 ARX Hs00292465_m1 CDX2 Hs00230919_m1 GAPDH Hs99999905_m1 GCG Hs00174967_m1 HNF4A Hs00230853_m1 INS Hs00355773_m1 ISL1 Hs00158126_m1 MAFA Hs01651425_s1 MAFB Hs00534343_s1 NEUROD1 Hs00159598_m1 NEUROG3 Hs00360700_g1 NKX2-2 Hs00159616_m1 NKX2-5 Hs00231763_m1 NKX6-1 Hs00232355_m1 PAX4 Hs00173014_m1 PAX6 Hs00240871_m1 PDX1 Hs00236830_m1 PECAM1 Hs00169777_m1 POU3F4 Hs00264887_s1 PTF1A Hs00603586_g1 SST Hs00356144_m1 ZIC1 Hs00602749_m1

TABLE 13 Differentiation Step 1 CT Values Treatment GAPDH AFP CD9 CD99 CDH1 CDH2 CDX2 CER1 CXCR4 FGF17 FGF4 FOXA2 GATA4 GATA6 AA/Wnt3a 19.5 34.7 23.8 24.1 24.5 21.5 36.8 18.4 22.7 20 33.5 24.7 23.7 22.1 GDF8/Wnt3a 18.7 36.1 23 23.5 23.3 21 36.2 17.8 21.9 19.9 33.1 23.8 23.7 21.9 GDF8/Compound 34 18.5 33 23 23.1 23.6 20.9 35.3 17.9 21.3 19.7 32.6 24 23.2 21.7 GDF8/Compound 56 17 31.2 20.8 20.9 21.2 18.4 35.3 15.5 19.4 17.2 29.7 21.1 20.8 19.6 Differentiation Step 1 CT Values Treatment GSC KIT MIXL1 MNX1 NANOG OTX2 POU5F1 SOX17 SOX7 T AA/Wnt3a 22.3 25 23.4 28 23.8 22.6 31.4 23.5 32.2 32.3 GDF8/Wnt3a 22.1 23.9 23.1 28.6 23 21.9 29.6 23.4 31.9 32.2 GDF8/Compound 34 21.9 24 23 27.5 23.2 21.5 30.1 23.2 31.7 32.1 GDF8/Compound 56 20 21.5 21.5 25 21.1 19.3 27.9 21.8 31.1 30.3 CT Values Treatment\CTs GAPDH ALB AMY2A ARX CDX2 GCG HNF4 INS ISL1 MAFA MAFB NEUROD1 NEUROG3 Differentiation Step 3 AA/Wnt3a 18.7 23.1 30.2 30.8 22.4 34.1 21.1 34.9 27.9 35.1 26.8 30.6 28 GDF8/Wnt3a 18.4 23.1 29.7 30.9 22.5 34.5 21.1 34.7 27.4 34.6 26.9 30.5 28 GDF8/Compound 34 18.4 23.3 29.7 34.7 22.5 36.6 21.1 38.1 27.5 34.2 26.8 33.3 31 GDF8/Compound 56 18.2 23.5 29.7 31.6 22.5 36.3 21.2 35.7 27.3 34.4 27 30.6 27.9 Differentiation Step 4 AA/Wnt3a 18.3 18.3 27.1 23.8 21.7 19.5 20.6 20.5 23.3 31 23.8 23 27.9 GDF8/Wnt3a 18.9 19.3 27.7 24.1 22.2 19.9 21.2 20.7 23.7 31.2 24.2 23.5 27.8 GDF8/Compound 34 18.9 18.9 27.1 25 22.3 21.5 21 22.2 24.4 31.3 24.6 24.6 29.7 GDF8/Compound 56 18.3 18.8 27.1 22.3 22.6 17.6 21.3 18.6 22.4 29.9 22.9 22.7 25.5 Differentiation Step 5 AA/Wnt3a 18.3 18.5 27.8 24 22.3 18.2 21.4 16.5 23.4 31.3 23.7 24.1 32.5 GDF8/Wnt3a 19.3 19.7 28.5 24.2 23.1 18.2 22 16.7 23.4 31.1 23.4 24.6 32.3 GDF8/Compound 34 19.9 20.6 29 24.1 23.7 17.8 22.4 16.3 23.7 31.3 24 24.4 32.4 GDF8/Compound 56 20 21.1 29 25.1 24.8 18.3 23.2 17.1 24.6 32.1 24.9 24.8 33.8 Differentiation Step 6 AA/Wnt3a 20.4 24.3 30.7 27.6 25.7 19.4 24.7 20.5 26.4 34.6 27.2 27.1 40 GDF8/Wnt3a 20.7 23.5 30.4 26.8 25.2 18.4 24.3 19.3 26.2 35.2 26.3 26.5 35 GDF8/Compound 34 21.3 24.6 31.3 27.1 26 18.4 24.7 20.1 26.3 34.8 26.4 27 34.5 GDF8/Compound 56 21.2 25 30.9 26 25.9 17.4 24.4 19.6 25.7 34.7 25.9 26.1 34.3 CT Values Treatment\CTs NKX2-2 NKX2-5 NKX6-1 PAX4 PAX6 PDX1 PECAM1 POU3F4 PTF1A SST ZIC1 Differentiation Step 3 AA/Wnt3a 29.3 33.1 38.5 30.6 36 25.6 28.3 29.5 38.4 30.3 32.7 GDF8/Wnt3a 30 36.4 36 31.1 33.5 25.4 30.4 30.1 38.5 27.9 32.4 GDF8/Compound 34 32.2 33.8 37.8 33.2 36.5 26.3 28.1 31.1 36.4 27.6 33.2 GDF8/Compound 56 30 33.8 38.2 30.8 32.7 25 28.9 30.4 34.8 27.5 32.7 Differentiation Step 4 AA/Wnt3a 24.6 31.5 31.5 27.5 26.4 24.1 26.9 27.6 40 25.2 31.4 GDF8/Wnt3a 25 35.4 31.5 27.7 26.3 24.5 29.5 29.3 38.2 24.9 31.4 GDF8/Compound 34 25.8 31.6 29.6 27.9 26.4 23.9 27.5 28.1 37.1 24.7 29.5 GDF8/Compound 56 23.2 32 27.9 25.5 23.8 23.2 27.8 27.5 30.9 22.8 32.1 Differentiation Step 5 AA/Wnt3a 25.4 29.7 32 28 25.1 24.2 26.9 29 37.5 22.5 29.9 GDF8/Wnt3a 25.6 29.9 30.5 28.1 25.4 24.6 29.9 29.9 33.4 22.1 32.1 GDF8/Compound 34 25.8 31.3 32 28.4 25.6 24.6 29.7 30.7 34.5 21.6 35 GDF8/Compound 56 26.3 34 30.2 29.7 27.3 25.9 29.7 31.5 34.7 22.1 33.3 Differentiation Step 6 AA/Wnt3a 29.6 30.7 33.4 30.9 28.6 29.2 31.3 32.8 38.4 22.2 34.8 GDF8/Wnt3a 29 32.3 30.5 30.7 27.8 28.5 32.3 31.5 33.9 22.4 27.4 GDF8/Compound 34 29.2 31.6 33.1 30.4 28.1 29 32.9 33.9 37.7 22.1 34.5 GDF8/Compound 56 28.1 33.8 30.7 29.3 27.2 27.9 33.6 33.2 35.2 21 34.9

TABLE 14 Differentiation Step 1 Ct Value Treatment GAPDH AFP CD9 CD99 CDH1 CDH CDX2 CER1 CXCR4 FGF17 FGF4 FOXA2 GATA4 GATA6 GSC AA/Wnt3a 20 35.6 24.1 24.2 26 20.9 40 17.5 22.7 19.8 35.8 24.7 23.8 22.1 21.6 GDF8/Wnt3a 20.1 34 23.8 24.5 24.6 21.6 40 19.5 23.3 21 34.8 25.1 24.5 23.3 23.3 GDF8/GSK3 inh 19 34.4 23.7 24.1 24.3 21.3 36 18.7 23 20.1 33.5 24.2 24.2 22.4 21.8 BIO GDF8/Compound 19.8 34.8 23.8 24 24.6 20.7 37.7 18.8 22.3 20 34.4 24.2 23.6 22.5 21.9 19 GDF8/Compound 19.8 40 24.5 23.5 25.9 20.8 40 18.8 22.2 20.3 36.5 24.4 23.4 22.3 22.3 202 GDF8/Compound 19.8 36.1 24.3 22.9 26.2 21.6 33.3 18.8 22.5 20.3 38.1 25.3 23.4 23 23 40 Differentiation Step 1 Ct Value Treatment HLXB9 KIT MIXL1 NANOG OTX2 POU5F1 SOX17 SOX7 T AA/Wnt3a 23.4 23.2 28.1 24.5 22 32.6 23.2 33 36.8 GDF8/Wnt3a 17.6 25.5 28.3 24.9 23 31 23.7 33.3 34.2 GDF8/GSK3 inh BIO 23.4 24.2 28.4 23.7 21.8 30.8 23 33.7 33.1 GDF8/Compound 19 23.1 24.3 28 24.3 21.8 31.3 22.3 33 32.9 GDF8/Compound 202 24 24.8 27.3 26 21.9 33.3 22.7 32.6 32.1 GDF8/Compound 40 25 25.7 27.8 26 22.3 32.8 23.2 27.2 29.3 Ct Value Treatment GAPDH ALB AMY2A ARX CDX2 GCG HNF4A INS ISL1 MAFA MAFB NEUROD1 NEUROG3 Differentiation Step 3 AA/Wnt3a 17.9 25.4 29.5 28.4 23.3 34.1 21.8 29.2 29.4 34 27 25.8 25.2 GDF8/Wnt3a 18.5 26.5 30.4 29.4 23.9 34.2 22.6 29 29 34.4 27.1 27.2 26.4 GDF8/GSK3 inh BIO 18.5 25.2 30.3 29.4 23.6 32.8 22.6 28.8 29.3 34.7 27.6 26.8 26.2 GDF8/Compound 19 18.4 26.1 30.2 29.1 24 33.1 22.5 28.5 30 34.4 27.3 26.6 25.9 GDF8/Compound 202 18.7 26.7 31.1 29.6 24 34.9 22.7 30.3 31.6 34.2 27.8 27.2 27 GDF8/Compound 40 18.6 25.8 30.5 29.6 23.8 37.6 22.5 30 31.1 34.5 27.9 27.2 26.2 Differentiation Step 4 AA/Wnt3a 18.9 21.3 28.8 24.6 23.4 21.7 21.9 21.6 25.2 32.4 24.9 23.7 23.8 GDF8/Wnt3a 18.3 21.3 28.5 25.3 23.1 22.6 21.9 21.9 25.7 33.1 24.9 24.3 24.2 GDF8/GSK3 inh BIO 19 21.1 28.7 25.3 23.3 22.3 21.9 22 25.7 32.5 25.4 24 24 GDF8/Compound 19 18.9 21.7 28.9 25.2 23.5 22.4 22.2 22 25.6 34 25.4 24.1 23.9 GDF8/Compound 202 19 20.9 29.2 25.1 23.6 22.4 22.1 22 25.5 33.3 25.5 23.9 24.1 GDF8/Compound 40 19.2 21.1 29.4 25.5 23.7 22.8 22.3 22.3 26 33.5 25.8 24.2 24.2 Differentiation Step 5 AA/Wnt3a 19.1 19.5 28.6 23.1 23.9 16.2 21.9 16.9 23.4 33.7 23.3 21.7 27.4 GDF8/Wnt3a 18.4 19.9 28.4 23.8 23.8 17.2 22.3 17.4 24 32.6 23.9 22.6 28.6 GDF8/GSK3 inh BIO 19.1 19.2 29.1 24 24.2 17.2 22.4 17.6 24 33.5 23.8 22.9 28.4 GDF8/Compound 19 19 20 28.8 23.4 24.2 17 22.6 17.1 23.8 33.2 23.8 22.8 28.6 GDF8/Compound 202 19.2 20 29 23 23.9 16.7 22.2 16.8 23.2 32.7 23.8 22.3 28.2 GDF8/Compound 40 19.6 19.5 29 23.7 24.2 16.9 22.2 17.1 23.9 33.2 23.9 22.5 28.1 Ct Value Treatment NKX2-2 NKX2-5 NKX6-1 PAX4 PAX6 PDX1 PECAM POU3F4 PTF1A SST ZIC1 Differentiation Step 3 AA/Wnt3a 27.3 34.1 28.3 27.8 35.2 22.7 28.3 28.6 30.8 32.2 37.4 GDF8/Wnt3a 27.9 37.8 29 29.2 31.4 23.3 32.2 30.1 30.7 31 30.1 GDF8/GSK3 inh BIO 27.6 35 28.8 28.7 32.9 23.2 32.2 29.5 30.6 31.3 31.1 GDF8/Compound 19 27.5 37.6 27.8 28.3 33.8 22.9 31.7 29.7 30 32.4 33.4 GDF8/Compound 202 28 40 30 29 36.2 23.7 30.9 30.2 32.4 32.4 34.6 GDF8/Compound 40 27.8 37.2 29.5 29 37.1 23.2 31.5 30.2 31.5 32.4 35.5 Differentiation Step 4 AA/Wnt3a 24.2 33.9 25.6 25.6 27 23 29.2 27 28.1 25.3 32.6 GDF8/Wnt3a 24.7 35.4 25.8 26.2 27.3 23.2 31.2 27 28.7 24.7 24.6 GDF8/GSK3 inh BIO 24.7 35.4 26.1 26 27.7 23.2 30.7 27.4 28.5 25.6 31.5 GDF8/Compound 19 24.6 35.9 25.7 25.7 27.8 23.1 31.4 27.1 28.6 25.5 31.4 GDF8/Compound 202 24.5 35.7 26 25.8 27.6 23.4 30.2 27.5 28.8 26.1 35.7 GDF8/Compound 40 24.6 37.3 25.9 25.9 28.4 23.1 30.4 27.6 28.4 26.3 34.4 Differentiation Step 5 AA/Wnt3a 24 33.1 25 26.4 24.7 22.6 27.1 28.4 27.5 22 34.1 GDF8/Wnt3a 24.2 33.1 25.8 27.2 25.6 23.6 29.2 28.9 29.1 22.7 25.6 GDF8/GSK3 inh BIO 24.4 40 25.1 27.3 25.6 23.6 29.2 28.1 28.7 23 26.3 GDF8/Compound 19 24.1 34.6 25 26.8 25.6 23.4 29.8 28.2 28.2 22.9 28.8 GDF8/Compound 202 23.2 40 26 27.2 25.8 23.4 29.9 29.1 28.4 22.6 33.8 GDF8/Compound 40 23.5 34.8 25 27.3 26.4 23.4 29.9 29.2 27.5 22.3 34.8

TABLE 15 Step 1 RT-PCR CT Values Treatment GAPDH AFP CD9 CD99 CDH1 CDH CDX2 CER1 CXCR4 FGF17 FGF4 FOXA2 GATA4 GATA6 AA 19.4 32.8 25.2 24.0 26.1 21.8 36.0 18.3 20.4 20.7 34.0 25.1 25.0 22.9 AA + Wnt3a 18.2 40.0 23.5 22.0 24.1 20.9 40.0 17.1 22.0 18.7 33.4 22.9 23.1 21.8 AA + Compound 181 20.1 40.0 24.5 23.3 26.0 20.7 35.9 18.2 22.0 20.1 35.1 25.6 24.7 22.9 AA + Compound 180 18.4 34.2 23.6 21.6 25.9 21.4 35.2 17.2 22.0 18.9 34.0 24.0 23.1 22.6 AA + Compound 19 20.1 35.4 24.4 24.9 26.3 20.8 40.0 17.9 17.7 20.5 32.8 25.6 25.1 22.7 AA + Compound 202 20.3 40.0 25.1 23.7 25.9 21.4 40.0 18.3 22.0 20.4 36.0 25.7 24.5 23.0 AA + Compound 40 19.9 40.0 24.6 23.6 25.8 20.4 40.0 17.7 22.7 20.2 35.1 25.5 24.6 22.5 AA + GSK3 inhib 20.2 35.0 25.4 23.7 27.2 21.9 35.5 18.5 22.2 20.9 36.0 25.8 25.0 23.2 BIO AA + Compound 206 19.8 40.0 24.9 23.7 25.5 21.1 40.0 18.3 19.6 20.7 36.2 24.4 24.8 22.7 GDF8 21.6 40.0 25.5 25.9 25.2 22.3 40.0 20.1 24.6 22.1 34.9 25.9 27.5 24.8 GDF8 + Wnt3a 21.2 40.0 25.0 25.8 25.1 22.6 40.0 19.7 23.6 22.0 34.8 25.7 27.3 24.4 GDF8 + Compound 181 20.7 40.0 25.1 23.6 25.5 22.4 40.0 20.0 23.0 21.5 36.3 25.2 25.4 23.9 GDF8 + Compound 180 20.9 40.0 25.6 24.0 26.9 22.1 34.7 19.9 22.7 21.1 36.6 25.0 25.2 23.9 GDF8 + Compound 19 19.6 40.0 23.9 23.7 24.6 20.7 40.0 18.0 21.8 20.4 33.2 24.2 25.0 22.8 GDF8 + Compound 202 18.5 30.6 22.1 20.2 22.8 19.7 35.8 18.5 22.4 19.9 34.3 23.6 22.7 22.5 GDF8 + Compound 40 19.7 40.0 23.0 22.6 24.7 20.5 33.8 18.2 22.4 20.5 35.4 24.9 24.2 22.6 GDF8 + GSK3 inhib 19.6 30.1 23.1 21.8 24.3 20.0 33.4 17.7 23.3 20.1 34.8 24.7 24.5 22.4 BIO GDF8 + Compound 206 19.7 40.0 22.7 22.5 23.2 21.0 29.9 18.4 23.0 20.3 34.5 25.3 24.9 22.9 Step 1 RT-PCR CT Values Treatment GSC HLXB9 KIT MIXL1 NANOG OTX2 POU5F1 SOX17 SOX7 T AA 22.4 24.8 22.7 28.9 24.1 22.5 32.2 21.6 32.3 36.1 AA + Wnt3a 22.8 23.3 22.9 27.7 22.7 19.9 31.0 21.2 31.2 34.1 AA + Compound 181 20.8 25.5 19.7 27.8 24.8 22.3 32.8 22.2 33.0 33.8 AA + Compound 180 22.5 24.8 22.6 27.9 23.7 20.3 32.1 21.4 32.0 32.7 AA + Compound 19 21.3 26.0 22.6 29.5 24.1 22.9 32.1 22.3 33.0 29.6 AA + Compound 202 21.8 25.2 23.9 27.7 24.5 22.5 32.7 22.6 32.1 33.5 AA + Compound 40 20.9 25.5 22.9 28.0 23.8 22.0 33.6 22.3 32.5 32.8 AA + GSK3 inhib BIO 22.2 25.2 23.7 28.5 24.9 22.8 34.3 23.4 32.7 33.5 AA + Compound 206 22.6 24.1 23.7 27.6 23.9 22.0 33.2 23.3 32.4 34.6 GDF8 24.2 25.3 25.4 30.6 25.0 24.3 29.5 25.2 29.8 32.9 GDF8 + Wnt3a 23.8 25.0 25.1 30.5 24.8 24.4 31.1 25.0 34.5 32.6 GDF8 + Compound 181 23.6 24.3 26.3 28.1 25.4 23.3 31.8 23.7 32.8 31.9 GDF8 + Compound 180 23.6 24.2 25.8 28.3 26.3 23.0 33.2 24.2 32.8 32.3 GDF8 + Compound 19 22.1 24.0 22.6 28.5 23.1 22.7 30.3 22.6 32.1 29.3 GDF8 + Compound 202 23.5 23.1 25.9 27.7 25.1 21.5 30.0 22.3 32.0 32.5 GDF8 + Compound 40 23.4 23.4 25.4 28.5 24.0 22.2 31.6 23.7 31.2 32.7 GDF8 + GSK3 inhib BIO 22.7 24.1 25.0 29.3 24.8 21.8 31.7 23.3 33.7 34.6 GDF8 + Compound 206 23.6 23.8 25.7 29.7 24.7 22.2 30.7 24.4 32.8 33.8 RT-PCR CT Values Treatment GAPDH ALB AMY2A ARX CDX2 GCG HNF4A INS ISL1 MAFA MAFB NEUROD1 NEUROG3 Step 3 AA 18.5 26.9 30.6 32.0 22.9 34.1 22.4 34.8 29.3 36.4 27.4 30.1 28.0 AA + Wnt3a 18.4 27.3 30.2 33.0 23.0 34.7 22.4 40.0 28.8 33.9 27.7 30.4 28.1 AA + Compound 181 18.6 26.0 30.1 34.2 22.3 40.0 22.3 40.0 30.4 34.6 28.5 31.4 29.0 AA + Compound 180 18.8 25.5 30.0 33.3 22.5 35.1 22.5 40.0 29.4 34.3 28.6 32.6 30.3 AA + Compound 19 34.1 40.0 40.0 40.0 40.0 40.0 37.4 40.0 40.0 40.0 34.9 40.0 40.0 AA + Compound 202 18.5 26.2 30.7 33.0 22.5 34.8 22.6 35.1 29.8 35.1 28.2 30.0 28.5 AA + Compound 40 18.5 25.8 30.1 34.9 22.2 40.0 22.3 40.0 29.7 34.1 28.1 30.8 29.1 AA + GSK3 inhib 18.5 24.9 30.1 34.6 22.0 40.0 21.5 40.0 30.2 34.9 27.8 34.0 31.0 BIO AA + Compound 206 18.3 27.0 30.3 33.7 22.7 35.7 22.5 40.0 28.4 34.4 27.8 30.7 28.6 GDF8 18.0 28.7 30.4 35.3 23.8 40.0 23.6 40.0 28.5 33.6 27.2 30.3 28.7 GDF8 + Wnt3a 17.4 27.0 29.5 33.8 23.1 35.1 22.4 40.0 26.3 30.5 26.1 30.1 27.5 GDF8 + Compound 18.8 27.8 30.2 31.3 23.4 40.0 22.7 34.5 28.8 35.5 27.3 28.9 27.0 181 GDF8 + Compound 18.8 27.3 30.6 32.4 22.8 34.9 22.7 40.0 29.5 35.9 27.7 30.0 27.5 180 GDF8 + Compound 19 18.3 24.9 29.7 33.4 22.0 40.0 22.2 40.0 29.7 34.5 28.4 33.3 31.5 GDF8 + Compound 18.7 27.8 30.4 32.8 23.8 40.0 22.9 34.6 28.5 34.2 27.6 29.6 27.1 202 GDF8 + Compound 40 18.4 27.7 30.1 32.5 23.0 35.1 22.4 40.0 29.1 34.3 27.5 30.0 27.3 GDF8 + GSK3 inhib 18.4 24.9 30.3 31.5 22.2 34.7 21.7 34.5 29.9 35.3 27.6 29.2 26.8 BIO GDF8 + Compound 18.2 27.6 30.2 33.5 23.8 40.0 22.9 40.0 27.9 35.1 27.1 29.9 27.7 206 Step 4 AA 19.0 22.4 28.6 23.9 23.7 22.8 22.1 23.6 24.1 30.6 23.5 23.7 23.3 AA + Wnt3a 19.5 23.5 29.3 24.6 24.1 25.1 22.7 25.2 25.1 31.1 24.4 24.4 24.1 AA + Compound 181 18.0 21.0 27.7 24.0 22.1 24.5 21.0 24.6 24.5 31.6 24.0 24.2 24.6 AA + Compound 180 19.4 21.0 27.3 26.3 21.6 25.4 20.6 26.7 26.1 34.7 24.6 25.5 25.8 AA + Compound 19 (insufficient RNA sample) AA + Compound 202 19.2 20.7 29.1 24.0 23.3 21.8 21.9 22.7 24.4 31.1 23.9 24.0 24.1 AA + Compound 40 19.2 20.8 29.4 24.7 22.9 22.2 21.8 23.5 25.3 31.5 24.7 24.7 25.3 AA + GSK3 inhib 19.0 19.1 29.2 26.7 22.7 25.2 21.1 26.3 26.5 33.0 25.4 26.3 27.7 BIO AA + Compound 206 18.8 20.9 28.4 23.3 22.9 21.2 21.7 22.8 24.0 30.4 23.5 23.3 23.3 GDF8 18.0 25.5 29.1 29.8 24.6 31.3 23.8 30.9 27.6 32.8 24.1 29.2 28.7 GDF8 + Wnt3a 19.0 24.3 29.0 25.4 24.4 27.7 23.0 25.5 25.4 32.7 25.1 25.4 24.0 GDF8 + Compound 18.0 22.8 28.1 23.5 23.1 24.6 21.4 22.7 23.8 30.6 23.0 22.9 21.8 181 GDF8 + Compound 19.5 24.0 29.3 24.4 23.9 25.7 22.5 24.5 24.7 31.4 24.4 24.3 23.7 180 GDF8 + Compound 19 19.1 22.6 28.7 25.5 22.9 26.7 22.1 27.2 25.8 32.6 25.5 26.2 26.4 GDF8 + Compound 19.0 22.0 28.9 23.7 24.5 21.8 22.3 21.7 24.3 30.3 23.5 22.9 22.2 202 GDF8 + Compound 40 19.0 21.4 29.0 23.4 23.6 21.0 22.0 21.5 23.8 30.2 23.3 23.2 22.7 GDF8 + GSK3 inhib 19.1 19.4 29.1 24.3 23.0 21.5 21.4 21.8 24.6 31.0 24.0 23.8 23.8 BIO GDF8 + Compound 18.9 21.6 28.9 24.4 24.0 22.6 22.3 22.7 24.9 30.9 24.2 23.7 23.0 206 Step 5 AA 18.3 20.2 27.6 22.0 23.4 14.1 21.3 14.9 22.4 31.8 22.2 22.8 28.1 AA + Wnt3a 18.0 20.0 27.7 21.9 23.1 14.0 20.9 14.6 22.3 31.6 22.0 21.6 28.0 AA + Compound 181 18.0 18.8 27.6 22.0 22.9 14.3 20.9 14.5 22.1 31.4 22.2 21.5 28.9 AA + Compound 180 18.0 18.8 27.6 22.4 22.9 14.9 21.0 14.7 22.4 31.9 22.6 21.7 29.5 AA + Compound 19 17.9 23.6 28.6 28.2 25.4 27.0 24.2 26.9 26.2 32.0 24.4 27.2 31.2 AA + Compound 202 18.6 19.2 28.0 22.6 23.4 14.9 21.3 15.0 22.7 31.8 22.6 21.9 28.6 AA + Compound 40 18.3 18.9 27.9 22.3 23.0 14.6 21.1 14.7 22.5 31.5 22.4 21.6 29.0 AA + GSK3 inhib 18.3 17.1 28.0 23.0 22.6 15.1 20.5 15.1 22.8 31.8 22.8 22.1 29.5 BIO AA + Compound 206 18.2 19.5 27.9 22.2 23.4 14.4 21.3 14.8 22.5 31.1 22.4 21.7 28.0 GDF8 17.4 20.5 28.2 25.2 24.4 18.1 22.9 17.7 24.3 31.8 23.3 24.2 30.1 GDF8 + Wnt3a 17.8 20.6 28.2 24.8 24.3 17.7 22.9 17.5 24.2 31.9 23.5 24.0 30.2 GDF8 + Compound 18.0 19.1 27.6 22.4 23.4 14.5 21.2 14.8 22.5 31.5 22.6 21.7 27.4 181 GDF8 + Compound 18.0 18.0 27.3 22.2 22.9 14.2 20.9 14.4 22.2 31.4 22.1 21.2 27.9 180 GDF8 + Compound 19 18.3 18.5 27.8 23.4 23.0 16.2 21.2 15.6 23.2 32.2 23.2 22.6 31.2 GDF8 + Compound 18.7 19.6 28.3 23.1 24.0 15.7 21.9 15.8 23.5 32.8 23.3 22.3 27.8 202 GDF8 + Compound 40 18.1 18.7 27.9 22.3 23.0 14.8 21.1 14.8 22.6 31.5 22.5 21.5 27.3 GDF8 + GSK3 inhib 18.4 17.1 27.6 23.2 22.8 15.2 20.6 15.5 23.1 32.6 22.6 22.1 28.2 BIO GDF8 + Compound 18.0 20.0 27.9 23.4 24.0 16.0 22.1 16.0 23.6 32.1 22.9 22.8 28.5 206 RT-PCR CT Values Treatment NKX2-2 NKX2-5 NKX6-1 PAX4 PAX6 PDX1 PECAM POU3F4 PTF1A SST ZIC1 Step 3 AA 29.3 34.6 32.2 31.4 40.0 23.3 31.0 30.5 34.6 33.2 34.8 AA + Wnt3a 29.0 40.0 34.9 31.9 38.1 23.8 30.9 30.7 40.0 32.8 40.0 AA + Compound 181 30.3 33.9 35.8 33.3 40.0 25.0 30.0 30.8 36.0 34.6 34.8 AA + Compound 180 31.1 32.5 35.3 35.3 36.2 26.3 28.9 31.3 40.0 34.7 34.4 AA + Compound 19 40.0 40.0 40.0 40.0 40.0 40.0 40.0 40.0 40.0 40.0 40.0 AA + Compound 202 29.5 33.6 33.9 32.0 36.6 24.1 29.7 31.9 40.0 34.2 40.0 AA + Compound 40 30.3 33.6 34.4 32.9 40.0 24.8 30.3 31.3 35.6 35.3 35.4 AA + GSK3 inhib BIO 31.8 32.6 40.0 34.9 40.0 26.1 31.0 32.4 40.0 35.2 34.9 AA + Compound 206 29.8 32.8 35.0 31.5 30.4 23.9 29.7 31.2 35.0 31.9 40.0 GDF8 30.3 34.4 35.0 32.4 24.8 25.5 30.0 30.8 34.2 29.5 26.1 GDF8 + Wnt3a 29.1 40.0 32.9 31.5 25.8 23.1 32.2 29.8 34.0 27.7 28.2 GDF8 + Compound 181 28.0 35.4 32.5 30.5 35.4 23.5 29.4 30.5 33.9 32.4 34.5 GDF8 + Compound 180 29.0 35.4 32.6 31.2 40.0 23.7 31.6 30.8 34.6 34.4 40.0 GDF8 + Compound 19 32.2 34.4 35.2 34.4 35.0 25.0 29.4 31.6 40.0 34.1 33.5 GDF8 + Compound 202 28.4 35.7 30.5 30.4 31.8 23.0 30.1 30.2 31.6 30.9 34.0 GDF8 + Compound 40 28.8 35.3 32.9 31.5 40.0 23.2 29.2 30.5 36.3 33.7 40.0 GDF8 + GSK3 inhib BIO 27.9 34.6 33.9 30.6 35.1 24.0 30.4 30.0 34.8 33.6 40.0 GDF8 + Compound 206 29.3 40.0 32.3 31.3 27.4 23.3 32.7 30.8 33.0 29.2 30.3 Step 4 AA 24.0 31.9 27.4 25.7 27.1 23.7 29.8 26.5 29.6 24.3 32.5 AA + Wnt3a 24.5 31.8 27.5 26.1 27.9 24.1 30.4 27.2 31.1 25.9 32.4 AA + Compound 181 24.6 30.9 28.1 26.3 28.0 24.0 27.9 27.5 31.0 25.5 31.2 AA + Compound 180 25.0 29.4 28.9 27.7 28.9 24.0 26.7 28.5 32.6 27.1 31.2 AA + Compound 19 (insufficient RNA sample) AA + Compound 202 24.4 32.1 27.4 26.3 26.9 24.3 29.6 27.7 29.5 24.0 35.1 AA + Compound 40 25.0 32.2 28.7 27.1 28.2 25.1 30.3 28.5 31.2 25.6 32.7 AA + GSK3 inhib BIO 26.2 31.5 32.9 29.4 30.0 26.5 29.6 30.5 33.7 27.2 32.4 AA + Compound 206 23.8 31.9 27.2 25.5 26.3 23.6 29.7 26.6 29.3 23.6 32.9 GDF8 29.0 32.3 31.2 31.1 27.9 26.5 29.4 29.4 40.0 26.0 22.8 GDF8 + Wnt3a 25.0 33.3 28.0 26.7 28.8 23.8 33.4 27.7 30.5 24.1 29.0 GDF8 + Compound 181 23.2 32.1 25.7 24.2 27.0 22.3 27.6 25.4 28.6 24.2 31.6 GDF8 + Compound 180 24.4 33.5 27.7 26.0 28.3 23.8 30.6 26.9 30.7 26.3 33.4 GDF8 + Compound 19 25.6 34.0 30.2 28.2 30.0 25.1 30.2 29.2 32.6 27.9 31.1 GDF8 + Compound 202 23.4 33.4 25.9 24.8 26.5 23.0 29.5 26.1 27.9 22.4 34.1 GDF8 + Compound 40 23.7 33.2 26.6 24.8 26.1 23.4 29.3 26.4 28.4 22.7 32.6 GDF8 + GSK3 inhib BIO 24.2 33.3 27.9 26.1 27.0 24.2 30.0 27.8 29.5 23.4 32.7 GDF8 + Compound 206 24.0 35.3 26.3 25.5 27.2 23.5 31.4 26.9 27.7 24.0 28.9 Step 5 AA 23.7 34.1 25.5 27.3 24.0 23.2 30.1 28.8 27.3 19.6 34.4 AA + Wnt3a 23.4 34.8 26.1 27.3 23.7 23.3 29.6 28.8 27.5 19.4 32.5 AA + Compound 181 23.3 32.2 26.1 26.8 24.0 23.1 27.5 28.8 28.0 18.8 31.2 AA + Compound 180 23.8 30.2 26.5 27.2 24.3 23.2 26.7 29.0 28.7 18.7 30.3 AA + Compound 19 28.0 30.1 25.8 35.1 28.6 29.4 31.5 28.2 32.4 23.1 24.0 AA + Compound 202 23.7 29.9 25.8 26.9 24.7 23.6 27.7 29.2 27.9 19.4 32.8 AA + Compound 40 23.5 32.9 26.1 27.1 24.4 23.2 28.1 29.2 28.1 19.1 31.9 AA + GSK3 inhib BIO 24.2 33.8 27.5 27.4 24.9 23.8 28.3 29.9 29.7 19.5 32.0 AA + Compound 206 23.6 35.8 25.9 27.1 24.1 23.3 29.0 28.7 27.5 19.7 32.7 GDF8 25.9 31.4 26.6 29.4 26.6 25.6 29.7 27.8 29.5 21.1 22.5 GDF8 + Wnt3a 25.6 31.9 27.0 29.3 26.5 25.6 29.8 28.1 30.7 21.5 22.8 GDF8 + Compound 181 23.4 33.8 25.0 26.8 24.4 23.0 27.5 28.8 27.3 19.5 31.9 GDF8 + Compound 180 23.2 40.0 25.1 26.1 23.8 22.9 29.6 28.7 27.3 18.8 31.5 GDF8 + Compound 19 24.3 33.9 28.6 27.3 25.2 24.2 29.0 30.1 31.0 20.5 31.9 GDF8 + Compound 202 23.8 31.3 24.8 27.1 25.2 23.2 29.0 29.5 27.1 20.8 30.9 GDF8 + Compound 40 23.2 33.2 25.0 26.6 24.1 22.9 27.3 28.9 27.4 20.4 32.0 GDF8 + GSK3 inhib BIO 24.2 35.0 26.7 27.3 24.8 24.0 28.1 30.1 28.5 19.3 32.4 GDF8 + Compound 206 24.4 30.5 25.9 27.5 25.4 24.0 29.7 28.3 28.0 20.8 23.9

TABLE 16 Compound # Primary Selectivity Compound 6 Selective for GSK Compound 7 Selective for GSK Compound 8 Selective for GSK Compound 9 Selective for CDK Compound 57 Selective for Trk Compound 41 Selective for GSK Compound 42 Selective for CDK Compound 10 Selective for CDK Compound 34 Positive Control Compound 11 Selective for CDK Compound 43 Selective for Trk Compound 44 Selective for GSK Compound 12 Selective for CDK Compound 45 Selective for Trk

TABLE 17 Cell Number Sox17 Expression % of Average Compound Average Total positive Total % of positive Plate Treatment Compound # Selectivity Cell Number control Intensity control 1 no Activin A none n/a 9809 67.8 −4.0E+05 −0.2 1 Activin A/Wnt3a none n/a 14476 100.0 2.3E+08 100.0 1 No GDF-8 Compound 11 Selective for CDK 565 3.9 −1.1E+06 −0.5 1 No GDF-8 Compound 44 Selective for GSK 14 0.1 −1.1E+06 −0.5 1 No GDF-8 Compound 43 Selective for Trk 8610 59.5 −2.1E+05 −0.1 1 No GDF-8 Compound 42 Selective for CDK 8700 60.1 −2.4E+05 −0.1 1 No GDF-8 Compound 57 Selective for Trk 1222 8.4 −7.1E+05 −0.3 1 No GDF-8 Compound 10 Selective for CDK 7011 48.4 −6.6E+05 −0.3 1 No GDF-8 Compound 41 Selective for GSK 9995 69.0 5.9E+04 0.0 1 No GDF-8 Compound 7 Selective for CDK 3 0.0 −1.4E+06 −0.6 1 No GDF-8 Compound 45 Selective for Trk 8857 61.2 −4.5E+05 −0.2 1 No GDF-8 Compound 6 Selective for GSK 14827 102.4 −1.8E+05 −0.1 1 No GDF-8 Compound 9 Selective for CDK 7156 49.4 −4.2E+04 0.0 1 No GDF-8 Compound 12 Selective for GSK 13124 90.7 −2.3E+05 −0.1 1 No GDF-8 Compound 8 Selective for GSK 13235 91.4 3.8E+05 0.2 1 GDF-8 Compound 34 Positive Control 13926 96.2 2.6E+08 111.8 1 GDF-8 Compound 45 Selective for Trk 9540 65.9 1.1E+08 47.9 1 GDF-8 Compound 7 Selective for GSK 5296 36.6 7.0E+07 30.4 1 GDF-8 Compound 10 Selective for CDK 4627 32.0 6.6E+07 28.6 1 GDF-8 Compound 6 Selective for GSK 5118 35.4 5.8E+07 25.2 1 GDF-8 Compound 43 Selective for Trk 6682 46.2 5.4E+07 23.4 1 GDF-8 Compound 42 Selective for CDK 5686 39.3 4.9E+07 21.2 1 GDF-8 Compound 8 Selective for GSK 5018 34.7 4.7E+07 20.4 1 GDF-8 Compound 9 Selective for CDK 4816 33.3 4.5E+07 19.4 1 GDF-8 Compound 41 Selective for GSK 4455 30.8 3.4E+07 14.8 1 GDF-8 n/a n/a 2856 19.7 2.2E+07 9.4 1 GDF-8 Compound 57 Selective for Trk 2110 14.6 1.1E+07 4.8 1 GDF-8 Compound 11 Selective for CDK 210 1.4 −4.9E+05 −0.2 1 GDF-8 Compound 44 Selective for GSK 226 1.6 −9.5E+05 −0.4 1 GDF-8 Compound 12 Selective for CDK 31 0.2 −1.3E+06 −0.6

TABLE 18 Cell Number Sox17 Expression Average % of Average % of Total Cell positive Total positive Plate Treatment Compound # Number SD CV % control Intensity SD CV % control 1 no Activin A (with Wnt3a) none 15489 0 0.00 103.2 3.75E+07 0.00E+00 0.00 10.9 1 Activin A/Wnt3a none 15007 1991 13.27 100.0 3.45E+08 7.16E+07 20.75 100.0 1 GDF-8 Compound 206 20568 1683 8.18 137.1 5.19E+08 4.41E+07 8.51 150.3 1 GDF-8 Compound 207 19224 1091 5.68 128.1 2.54E+08 5.69E+07 22.41 73.6 1 GDF-8 Compound 19 12569 1524 12.13 83.8 2.40E+08 6.34E+07 26.44 69.5 1 GDF-8 Compound 23 8758 474 5.41 58.4 1.16E+08 9.07E+06 7.80 33.7 1 GDF-8 Compound 170 6460 2305 35.68 43.0 9.44E+07 6.98E+07 73.93 27.4 1 GDF-8 Compound 208 4848 1225 25.27 32.3 2.26E+07 2.15E+07 94.96 23.6 1 GDF-8 Compound 209 4831 1243 25.74 32.2 3.97E+07 1.61E+07 40.56 11.5 1 GDF-8 Compound 32 4338 1520 35.04 28.9 3.63E+07 3.27E+07 90.14 10.5 1 GDF-8 Compound 30 4679 435 9.29 31.2 3.47E+07 1.04E+07 30.03 10.1 1 GDF-8 Compound 223 3704 1077 29.08 24.7 3.45E+07 2.74E+07 79.43 10.0 1 GDF-8 Compound 2 4538 632 13.93 30.2 2.95E+07 2.81E+06 9.50 8.6 1 GDF-8 Compound 210 2645 817 30.88 17.6 2.90E+07 2.45E+07 84.73 8.4 1 GDF-8 Compound 24 5012 1263 25.21 33.4 2.64E+07 1.66E+07 62.95 7.7 1 GDF-8 Compound 211 5165 796 15.41 34.4 2.61E+07 5.02E+06 19.23 7.6 1 GDF-8 Compound 212 5476 1445 26.39 36.5 2.54E+07 1.18E+07 46.53 7.4 1 GDF-8 Compound 224 5188 761 14.67 34.6 2.46E+07 8.26E+06 33.56 7.1 1 GDF-8 Compound 225 4431 1149 25.92 29.5 2.45E+07 2.65E+07 108.19 7.1 1 GDF-8 Compound 13 3123 1508 48.27 20.8 2.44E+07 2.30E+07 94.13 7.1 1 GDF-8 Compound 213 1261 1028 81.49 8.4 2.07E+07 1.97E+07 95.03 6.0 1 GDF-8 Compound 52 4932 386 7.82 32.9 1.99E+07 6.90E+06 34.67 5.8 1 GDF-8 Compound 214 3345 335 10.01 22.3 1.93E+07 1.39E+07 72.18 5.6 1 GDF-8 Compound 51 4289 940 21.91 28.6 1.70E+07 1.10E+07 64.86 4.9 1 GDF-8 Compound 26 4896 545 11.14 32.6 1.65E+07 5.93E+06 36.02 4.8 1 GDF-8 Compound 226 3617 577 15.94 24.1 1.59E+07 4.96E+06 31.21 4.6 1 GDF-8 Compound 215 4326 165 3.81 28.8 1.45E+07 2.69E+06 18.53 4.2 1 GDF-8 Compound 31 3619 1011 27.92 24.1 1.36E+07 4.63E+06 34.15 3.9 1 GDF-8 Compound 216 3364 629 18.70 22.4 8.75E+06 2.30E+06 26.32 2.5 1 GDF-8 Compound 217 2859 544 19.03 19.1 8.75E+06 1.94E+06 22.16 2.5 1 GDF-8 Compound 218 1327 118 8.92 8.8 6.44E+06 9.70E+05 15.05 1.9 1 GDF-8 Compound 219 368 168 45.67 2.5 1.79E+06 1.29E+06 72.17 0.5 2 no Activin A (with Wnt3a) none 15778 0 0.00 103.2 2.24E+07 0.00E+00 0.00 6.7 2 Activin A/Wnt3a none 15290 1119 7.32 100.0 3.37E+08 2.84E+07 8.44 100.0 2 GDF-8 Compound 202 20177 987 4.89 132.0 4.85E+08 1.94E+07 4.00 144.0 2 GDF-8 Compound 227 2911 4619 158.69 19.0 3.89E+07 6.69E+07 172.00 11.5 2 GDF-8 Compound 15 4383 1775 40.49 28.7 3.57E+07 3.57E+07 100.03 10.6 2 GDF-8 Compound 228 4043 1253 30.98 26.4 3.10E+07 2.53E+07 81.62 9.2 2 GDF-8 Compound 229 3451 892 25.85 22.6 1.80E+07 1.46E+07 81.07 5.4 2 GDF-8 Compound 4 3163 805 25.44 20.7 1.58E+07 3.54E+06 22.32 4.7 2 GDF-8 Compound 220 2791 1453 52.05 18.3 1.40E+07 9.00E+06 64.28 4.2 2 GDF-8 Compound 5 3137 1172 37.34 20.5 1.30E+07 7.52E+06 57.85 3.9 2 GDF-8 Compound 230 2624 248 9.46 17.2 1.24E+07 1.55E+07 124.73 3.7 2 GDF-8 Compound 231 4773 2651 55.55 31.2 1.22E+07 6.51E+06 53.37 3.6 2 GDF-8 Compound 232 3273 1290 39.41 21.4 1.18E+07 1.51E+07 127.98 3.5 2 GDF-8 Compound 221 1950 361 18.52 12.8 1.18E+07 1.54E+07 131.11 3.5 2 GDF-8 Compound 233 3041 180 5.93 19.9 1.12E+07 1.09E+07 97.44 3.3 2 GDF-8 Compound 147 3434 1199 34.91 22.5 1.12E+07 9.80E+06 87.75 3.3 2 GDF-8 Compound 234 2835 623 21.98 18.5 9.47E+06 5.67E+06 59.84 2.8 2 GDF-8 Compound 235 3391 2269 66.91 22.2 9.10E+06 6.51E+06 71.52 2.7 2 GDF-8 Compound 236 2868 561 19.57 18.8 6.73E+06 6.32E+06 93.82 2.0 2 GDF-8 Compound 33 2362 511 21.66 15.4 6.60E+06 2.45E+06 37.20 2.0 2 GDF-8 Compound 1 3213 166 5.16 21.0 6.48E+06 3.09E+06 47.67 1.9 2 GDF-8 Compound 53 2783 441 15.86 18.2 6.36E+06 2.89E+06 45.36 1.9 2 GDF-8 Compound 237 2973 292 9.83 19.4 6.02E+06 3.00E+06 49.79 1.8 2 GDF-8 Compound 238 2739 485 17.70 17.9 5.97E+06 6.10E+06 102.07 1.8 2 GDF-8 Compound 239 3156 667 21.15 20.6 5.60E+06 2.42E+06 43.24 1.7 2 GDF-8 Compound 240 3002 287 9.55 19.6 4.68E+06 3.13E+06 66.80 1.4 2 GDF-8 Compound 200 2308 209 9.04 15.1 4.39E+06 1.88E+06 42.83 1.3 2 GDF-8 Compound 222 1776 719 40.47 11.6 3.33E+06 2.52E+06 75.78 1.0 2 GDF-8 Compound 241 2949 446 15.14 19.3 3.29E+06 1.55E+06 47.03 1.0 2 GDF-8 Compound 242 385 184 47.83 2.5 1.08E+06 8.85E+05 81.61 0.3 2 GDF-8 Compound 243 249 55 22.21 1.6 2.53E+05 3.07E+05 121.25 0.1 2 GDF-8 Compound 204 250 21 8.38 1.6 1.36E+05 2.27E+04 16.66 0.0 3 no Activin A (with Wnt3a) none 15796 0 0.00 99.6 2.82E+07 0.00E+00 0.00 8.0 3 Activin A/Wnt3a none 15867 785 4.95 100.0 3.54E+08 2.40E+07 6.77 100.0 3 GDF-8 Compound 34 6974 3723 53.38 44.0 2.07E+08 9.51E+07 45.85 58.6 3 GDF-8 Compound 185 10892 1552 14.24 68.6 1.53E+08 4.08E+07 26.72 43.1 3 GDF-8 Compound 35 7746 1873 24.17 48.8 1.35E+08 4.86E+07 36.08 38.0 3 GDF-8 Compound 22 6727 1927 28.64 42.4 1.06E+08 5.04E+07 47.73 29.8 3 GDF-8 Compound 34 4889 1152 23.57 30.8 4.31E+07 2.11E+07 48.95 12.2 3 GDF-8 Compound 184 4173 1758 42.14 26.3 3.94E+07 2.24E+07 56.78 11.1 3 GDF-8 Compound 223 4234 1604 37.88 26.7 3.55E+07 2.51E+07 70.56 10.0 3 GDF-8 Compound 37 4187 338 8.06 26.4 3.11E+07 1.56E+07 50.18 8.8 3 GDF-8 Compound 244 4479 1229 27.43 28.2 2.73E+07 1.52E+07 55.71 7.7 3 GDF-8 Compound 245 4725 99 2.09 29.8 2.59E+07 1.03E+07 39.90 7.3 3 GDF-8 Compound 246 3820 1091 28.57 24.1 2.30E+07 2.69E+07 117.08 6.5 3 GDF-8 Compound 247 3730 966 25.90 23.5 2.14E+07 1.04E+07 48.63 6.1 3 GDF-8 Compound 248 3875 445 11.48 24.4 2.13E+07 9.45E+06 44.45 6.0 3 GDF-8 Compound 25 3879 658 16.95 24.4 1.76E+07 1.21E+07 69.04 5.0 3 GDF-8 Compound 195 3703 405 10.94 23.3 1.61E+07 3.27E+06 20.34 4.5 3 GDF-8 Compound 227 2904 397 13.68 18.3 1.43E+07 1.35E+07 94.25 4.0 3 GDF-8 Compound 183 3306 969 29.32 20.8 1.35E+07 1.14E+07 84.25 3.8 3 GDF-8 Compound 187 2768 1426 51.51 17.4 1.35E+07 9.02E+06 66.67 3.8 3 GDF-8 Compound 201 3213 1114 34.66 20.3 1.35E+07 1.69E+07 125.02 3.8 3 GDF-8 Compound 197 3268 211 6.46 20.6 1.30E+07 5.25E+06 40.51 3.7 3 GDF-8 Compound 249 3840 348 9.06 24.2 1.29E+07 6.79E+06 52.72 3.6 3 GDF-8 Compound 141 2404 213 8.86 15.1 1.12E+07 4.95E+06 44.30 3.2 3 GDF-8 Compound 194 3177 354 11.14 20.0 9.75E+06 2.11E+06 21.63 2.8 3 GDF-8 Compound 250 3683 420 11.40 23.2 9.14E+06 4.78E+06 52.32 2.6 3 GDF-8 Compound 251 3021 668 22.10 19.0 8.41E+06 4.59E+06 54.60 2.4 3 GDF-8 Compound 20 2793 205 7.35 17.6 6.77E+06 1.86E+06 27.45 1.9 3 GDF-8 Compound 252 2580 135 5.24 16.3 6.20E+06 2.31E+05 3.72 1.8 3 GDF-8 Compound 253 2485 820 32.98 15.7 5.83E+06 1.47E+06 25.20 1.6 3 GDF-8 Compound 202 2095 518 24.71 13.2 5.75E+06 2.62E+06 45.66 1.6 3 GDF-8 Compound 21 371 294 79.19 2.3 2.36E+06 3.07E+06 129.78 0.7 4 no Activin A (with Wnt3a) none 16629 0 0.00 119.3 2.42E+07 0.00E+00 0.00 7.8 4 Activin A/Wnt3a none 13945 1535 11.01 100.0 3.09E+08 4.77E+07 15.46 100.0 4 GDF-8 Compound 34 7416 6482 87.41 53.2 2.10E+08 1.82E+08 86.70 68.0 4 GDF-8 Compound 240 11283 2023 17.93 80.9 1.61E+08 4.41E+07 27.34 52.2 4 GDF-8 Compound 28 5236 1787 34.12 37.5 4.03E+07 3.08E+07 76.36 13.1 4 GDF-8 Compound 198 3985 2674 67.10 28.6 3.89E+07 5.55E+07 142.91 12.6 4 GDF-8 Compound 196 4861 1501 30.87 34.9 3.03E+07 1.98E+07 65.37 9.8 4 GDF-8 Compound 18 1921 1759 91.56 13.8 2.94E+07 3.65E+07 123.90 9.5 4 GDF-8 Compound 186 3486 425 12.19 25.0 2.34E+07 1.42E+07 60.78 7.6 4 GDF-8 Compound 254 3960 1521 38.42 28.4 2.31E+07 2.27E+07 98.10 7.5 4 GDF-8 Compound 168 3460 324 9.36 24.8 2.28E+07 7.13E+06 31.23 7.4 4 GDF-8 Compound 190 3402 1318 38.74 24.4 1.87E+07 1.58E+07 84.61 6.1 4 GDF-8 Compound 255 4006 1625 40.57 28.7 1.52E+07 1.05E+07 68.91 4.9 4 GDF-8 Compound 50 2666 743 27.86 19.1 1.48E+07 8.30E+06 56.15 4.8 4 GDF-8 Compound 27 3721 721 19.37 26.7 1.19E+07 9.69E+06 81.29 3.9 4 GDF-8 Compound 256 2922 1275 43.64 21.0 9.41E+06 8.65E+06 92.01 3.0 4 GDF-8 Compound 257 3182 705 22.14 22.8 8.06E+06 4.49E+06 55.75 2.6 4 GDF-8 Compound 258 2731 472 17.29 19.6 7.89E+06 7.24E+06 91.70 2.6 4 GDF-8 Compound 189 2350 1625 69.16 16.9 7.72E+06 5.36E+06 69.41 2.5 4 GDF-8 Compound 259 2195 955 43.49 15.7 6.92E+06 2.58E+06 37.29 2.2 4 GDF-8 Compound 260 2468 741 30.04 17.7 6.64E+06 3.33E+06 50.18 2.2 4 GDF-8 Compound 261 2965 456 15.38 21.3 6.23E+06 2.10E+06 33.61 2.0 4 GDF-8 Compound 192 2377 572 24.08 17.0 6.17E+06 2.76E+06 44.65 2.0 4 GDF-8 Compound 262 2894 399 13.78 20.8 5.75E+06 3.00E+06 52.20 1.9 4 GDF-8 Compound 188 3005 759 25.26 21.6 5.02E+06 3.97E+06 79.06 1.6 4 GDF-8 Compound 263 2129 230 10.79 15.3 4.77E+06 1.14E+06 23.93 1.5 4 GDF-8 Compound 264 2630 342 13.00 18.9 4.28E+06 2.17E+06 50.73 1.4 4 GDF-8 Compound 265 2636 1372 52.04 18.9 4.27E+06 1.15E+06 26.86 1.4 4 GDF-8 Compound 14 274 14 5.02 2.0 1.56E+05 9.51E+04 60.91 0.1 4 GDF-8 Compound 205 241 3 1.20 1.7 1.36E+05 6.83E+04 50.42 0.0 4 GDF-8 Compound 266 271 7 2.67 1.9 1.18E+05 3.34E+04 28.43 0.0 4 GDF-8 Compound 203 253 4 1.49 1.8 1.09E+05 3.49E+04 32.09 0.0

TABLE 19 Sox 17 Expression Compound # % of positive control Compound 181 150.3 Compound 202 144.0 Compound 180 73.6 Compound 19 69.5 Compound 34 68.0 Compound 40 52.2 Compound 185 43.1 Compound 185 38.0 Compound 35 33.7 Compound 23 29.8 Compound 22 27.4 Compound 17 23.6 

What is claimed is:
 1. A method to differentiate pluripotent stem cells into definitive endoderm cells comprising culturing the pluripotent stem cells with a medium supplemented with activin A, Wnt3a, 5-chloro-1,8,10,12,16,22,26,32-octaazapentacyclo[24.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜] tritriaconta-3(33),4,6,9(32),10,12,14(31),15,17-nonaen-23-one and one or more of EGF and FGF4.
 2. The method of claim 1, wherein the medium is supplemented with activin A, Wnt3a, 5-chloro-1,8,10,12,16,22,26,32-octaazapentacyclo[24.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜] tritriaconta-3(33),4,6,9(32),10,12,14(31),15,17-nonaen-23-one and EGF.
 3. The method of claim 1, wherein the medium is supplemented with activin A, Wnt3a, 5-chloro-1,8,10,12,16,22,26,32-octaazapentacyclo[24.2.2.1˜3,7˜.1˜9,13˜.1-14,18˜] tritriaconta-3(33),4,6,9(32),10,12,14(31),15,17-nonaen-23-one and FGF-4.
 4. The method of claim 1, wherein the medium is supplemented with activin A, Wnt3a, 5-chloro-1,8,10,12,16,22,26,32-octaazapentacyclo[24.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜] tritriaconta-3(33),4,6,9(32),10,12,14(31),15,17-nonaen-23-one EGF and FGF-4.
 5. The method of claim 4, wherein the medium is further supplemented with PDGF-AB.
 6. The method of claim 5 wherein the medium is further supplemented with VEGF.
 7. The method of claim 4, wherein the medium is further supplemented with GDF-8 and muscimol.
 8. The method of claim 4, wherein the medium is further supplemented with PDFG-A, VEGF, PDGF, muscimol and GDF-8.
 9. The method of claim 1, wherein the pluripotent stem cells are human pluripotent stem cells.
 10. The method of claim 9, wherein the human pluripotent stem cells are human embryonic stem cells.
 11. A method to differentiate pluripotent stem cells into definitive endoderm cells comprising culturing the pluripotent stem cells with a medium supplemented with activin A and 5-chloro-1,8,10,12,16,22,26,32-octaazapentacyclo[24.2.2.1˜3,7˜.1˜9,13˜.1˜14,18˜] tritriaconta-3(33),4,6,9(32),10,12,14(31),15,17-nonaen-23-one.
 12. The method of claim 11, wherein the medium is further supplemented with Wnt3a.
 13. The method of claim 11, wherein the pluripotent stem cells are human pluripotent stem cells.
 14. The method of claim 13, wherein the human pluripotent stem cells are human embryonic stem cells. 